Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008103.1 Hibiscus syriacus cultivar Beakdansim tig00110633_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: 1996589
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:360770 original size:13 final size:14
Alignment explanation
Indices: 360742--360774 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
360732 GTGTTTTTTA
360742 TTTTATTAACATTT
1 TTTTATTAACATTT
*
360756 TTTTCTTAACATTT
1 TTTTATTAACATTT
360770 TTTTA
1 TTTTA
360775 CTTACAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTAACATTT
Found at i:360773 original size:15 final size:15
Alignment explanation
Indices: 360737--360778 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
360727 TTTCAGTGTT
*
360737 TTTTATTTTATTAACA
1 TTTT-TTTTCTTAACA
360753 -TTTTTTTCTTAACA
1 TTTTTTTTCTTAACA
*
360767 TTTTTTTACTTA
1 TTTTTTTTCTTA
360779 CAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTTCTTAACA
Found at i:360873 original size:14 final size:14
Alignment explanation
Indices: 360854--360896 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
360844 TATATTTACC
* *
360854 TTTATTTGTTTGTT
1 TTTATTTATTTATT
360868 TTTATTTATTTATT
1 TTTATTTATTTATT
*
360882 TTTATTTATATATT
1 TTTATTTATTTATT
360896 T
1 T
360897 CACCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:360877 original size:18 final size:18
Alignment explanation
Indices: 360806--360896 Score: 53
Period size: 18 Copynumber: 4.8 Consensus size: 18
360796 TTTCTTCTTC
360806 TTATTTATTTA-TTATTT
1 TTATTTATTTATTTATTT
*
360823 CGTT-TTTATTATATTCGTAATT
1 --TTATTTATT-TATT--TATTT
* *
360845 ATATTTACCTTTATTTGTTT
1 TTATTTA--TTTATTTATTT
360865 GTT-TTTATTTATTTATTT
1 -TTATTTATTTATTTATTT
*
360883 TTATTTATATATTT
1 TTATTTATTTATTT
360897 CACCATTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
17 2 0.04
18 26 0.46
19 4 0.07
20 9 0.16
21 5 0.09
22 8 0.14
23 2 0.04
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (18 bp):
TTATTTATTTATTTATTT
Found at i:360987 original size:12 final size:12
Alignment explanation
Indices: 360970--360996 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
360960 GAATCGAAAC
360970 TTTAAATTTCAA
1 TTTAAATTTCAA
360982 TTTAAATTTCAA
1 TTTAAATTTCAA
360994 TTT
1 TTT
360997 TTCGCAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:367781 original size:38 final size:38
Alignment explanation
Indices: 367723--367818 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 38
367713 CTCGTATAAA
*
367723 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
* * *
367761 TGTCTCGAAGGACCTGTCATCTCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
367799 TGTCCCGTAA-GACCTATCAT
1 TGTCCCG-AAGGACCTATCAT
367819 ATGTCCTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 49 0.96
39 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:368024 original size:46 final size:45
Alignment explanation
Indices: 367967--368071 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 45
367957 ATGTGTAACC
*
367967 ATGTATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTATTTCATATCATATCACATGTATCACATATTACATATTCAT
*
368012 ATGTCATTTCATATCATATCACATGTATCACATATTGCATATTCAT
1 ATGT-ATTTCATATCATATCACATGTATCACATATTACATATTCAT
*
368058 ATATAATTTCATAT
1 ATGT-ATTTCATAT
368072 AGTCATATAG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 4 0.07
46 51 0.93
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (45 bp):
ATGTATTTCATATCATATCACATGTATCACATATTACATATTCAT
Found at i:369311 original size:2 final size:2
Alignment explanation
Indices: 369293--369329 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
369283 GGGATGTTAC
* *
369293 AT AT CT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
369330 ACTTAGGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:370706 original size:3 final size:3
Alignment explanation
Indices: 370681--370739 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
370671 TGTAAACCCT
*
370681 ATA AAA ATA ATA GA-A ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
370725 AT- ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA A
370740 GGGTAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 5 0.10
3 42 0.88
4 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:373281 original size:2 final size:2
Alignment explanation
Indices: 373274--373300 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
373264 TCCTTAAATA
373274 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
373301 AATCTAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:375177 original size:19 final size:19
Alignment explanation
Indices: 375132--375179 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
375122 ATCTCTTGAA
* *
375132 ATTAATAAATTATTAATTT
1 ATTAATTAATTAATAATTT
*
375151 ATTGATTAATTAATATATTT
1 ATTAATTAATTAATA-ATTT
375171 -TTAATTAAT
1 ATTAATTAAT
375180 AAAATTATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTAATTAATTAATAATTT
Found at i:385241 original size:2 final size:2
Alignment explanation
Indices: 385234--385277 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
385224 TTCATTAACC
385234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
385276 AT
1 AT
385278 TTCTATGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386978 original size:21 final size:22
Alignment explanation
Indices: 386952--386996 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
386942 GAATGCAAAT
386952 AGGGAATCG-GTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
386973 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
386995 AG
1 AG
386997 TACTACTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:387428 original size:19 final size:19
Alignment explanation
Indices: 387404--387440 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
387394 ATGACCAACA
387404 AAATCGCAA-TGCGATCTCT
1 AAATCGCAACT-CGATCTCT
387423 AAATCGCAACTCGATCTC
1 AAATCGCAACTCGATCTC
387441 CATTATCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATCGCAACTCGATCTCT
Found at i:387578 original size:20 final size:20
Alignment explanation
Indices: 387536--387578 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
387526 AATCGTAAAT
*
387536 CGAATATGTAAATCACAATG
1 CGAATATGTAAATCACAACG
*
387556 CGAATATGTAAATCGCAACG
1 CGAATATGTAAATCACAACG
387576 CGA
1 CGA
387579 TAACACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
CGAATATGTAAATCACAACG
Found at i:387825 original size:22 final size:22
Alignment explanation
Indices: 387800--387871 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
387790 TCTACGCGAC
387800 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
387822 ATCCGTCCCCATTTACGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * **
387844 AT-CATCCCCATCTCTGGTGAA
1 ATCCGTCCCCATCTCCGACGAA
387865 ATCCGTC
1 ATCCGTC
387872 TATCTCCATC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 15 0.38
22 25 0.62
ACGTcount: A:0.24, C:0.39, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:387853 original size:21 final size:22
Alignment explanation
Indices: 387790--387856 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
387780 TCTCTCACTC
* *
387790 TCTACG-CGACATCCGTCCCCA
1 TCTACGACGAAATCCATCCCCA
* *
387811 TCTCCGACGAAATCCGTCCCCA
1 TCTACGACGAAATCCATCCCCA
*
387833 TTTACGACGAAAT-CATCCCCA
1 TCTACGACGAAATCCATCCCCA
387854 TCT
1 TCT
387857 CTGGTGAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.36
22 25 0.64
ACGTcount: A:0.24, C:0.42, G:0.12, T:0.22
Consensus pattern (22 bp):
TCTACGACGAAATCCATCCCCA
Found at i:388317 original size:20 final size:20
Alignment explanation
Indices: 388269--388319 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
388259 TCAAATTCAC
**
388269 GTTGCGATAATCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
388289 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
388309 GTTGCGATTTT
1 GTTGCGATTTT
388320 AAGTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:388326 original size:20 final size:20
Alignment explanation
Indices: 388283--388326 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
388273 CGATAATCAT
* *
388283 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
388303 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
388323 TTTC
1 TTTC
388327 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:390193 original size:31 final size:31
Alignment explanation
Indices: 390137--390198 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
390127 TTGTCTTTGT
*
390137 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
390169 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
390199 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:390381 original size:34 final size:34
Alignment explanation
Indices: 390335--390471 Score: 130
Period size: 34 Copynumber: 3.9 Consensus size: 34
390325 CGAAAATATT
* ** *
390335 ATCGCAACGTGAATTTGACTATCGCAAAGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACGGGATA
* * *
390369 ATCGCAATGTGAAAACGACTATCGCAACGCGGAAATGA
1 ATCGCAACGCGAAAATGACTATCGCAACG-GG--AT-A
**
390407 CTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 --ATCGCAACGCGAAAATGACTATCGCAACGGGATA
*
390443 ATCGCAATGCGAAAATGACTATCGCAACG
1 ATCGCAACGCGAAAATGACTATCGCAACG
390472 CGAATTTAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
34 50 0.60
35 2 0.02
36 1 0.01
37 4 0.05
38 1 0.01
39 2 0.02
40 24 0.29
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACGGGATA
Found at i:390457 original size:74 final size:73
Alignment explanation
Indices: 390317--390475 Score: 246
Period size: 74 Copynumber: 2.2 Consensus size: 73
390307 AGAAGAATAG
* * * *
390317 TCGCAACACGAAAATATTATCGCAACGTGAATTTGACTATCGCAAAGGGATAATCGCAATGTGAA
1 TCGCAACGCGAAAATACTATCGCAACGCGAATTTGACTATCGCAAAGGGATAATCGCAATGCGAA
390382 AACGACTA
66 AACGACTA
* *
390390 TCGCAACGCGGAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
1 TCGCAACGCGAAAAT-ACTATCGCAACGCGAATTTGACTATCGCAAAGGGATAATCGCAATGCGA
*
390455 AAATGACTA
65 AAACGACTA
390464 TCGCAACGCGAA
1 TCGCAACGCGAA
390476 TTTAGTTTCG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 13 0.17
74 64 0.83
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (73 bp):
TCGCAACGCGAAAATACTATCGCAACGCGAATTTGACTATCGCAAAGGGATAATCGCAATGCGAA
AACGACTA
Found at i:390468 original size:20 final size:20
Alignment explanation
Indices: 390369--390475 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
390359 CAAAGGGATA
* * *
390369 ATCGCAATGTGAAAACGACT
1 ATCGCAACGCGAAAATGACT
*
390389 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
390409 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
390429 ATCGCAACG-G--GAT-A--
1 ATCGCAACGCGAAAATGACT
*
390443 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
390463 ATCGCAACGCGAA
1 ATCGCAACGCGAA
390476 TTTAGTTTCG
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
14 8 0.12
15 1 0.01
16 1 0.01
17 3 0.04
18 1 0.01
19 1 0.01
20 54 0.78
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:390493 original size:19 final size:19
Alignment explanation
Indices: 390471--390507 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
390461 CTATCGCAAC
390471 GCGAATTTAGTTTCGCGTA
1 GCGAATTTAGTTTCGCGTA
* *
390490 GCGATTTTGGTTTCGCGT
1 GCGAATTTAGTTTCGCGT
390508 TGTGATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.41
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTA
Found at i:390537 original size:33 final size:34
Alignment explanation
Indices: 390500--390580 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 34
390490 GCGATTTTGG
* *
390500 TTTCGCGTTGTGATTTTCTCGTTGCGATAGTC-A
1 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
*
390533 TTTCGTGTTGCGATTATCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
*
390567 ATTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
390581 AGTCAAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.69
34 13 0.31
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (34 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
Found at i:390577 original size:20 final size:20
Alignment explanation
Indices: 390552--390601 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
390542 GCGATTATCT
390552 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
390572 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
390592 CGTTGCGATA
1 CGTTGCGATA
390602 ATCATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:390634 original size:20 final size:20
Alignment explanation
Indices: 390611--390650 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
390601 AATCATTTTT
390611 GTGTTGCAATTTTAAGTTTC
1 GTGTTGCAATTTTAAGTTTC
*
390631 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCAATTTTAAGTTTC
390651 AGAAACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCAATTTTAAGTTTC
Found at i:391181 original size:21 final size:21
Alignment explanation
Indices: 391157--391215 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
391147 CTCCTATCGT
391157 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCT-TCATCCGC
* * *
391178 TCAAGAGTCCCCTCCA-CCGT
1 TCAAGAGGCCCCTTCATCCGC
391198 TCAAGAGGCCCCTGTCAT
1 TCAAGAGGCCCCT-TCAT
391216 TGTTGAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.07
20 14 0.47
21 14 0.47
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (21 bp):
TCAAGAGGCCCCTTCATCCGC
Found at i:391232 original size:41 final size:42
Alignment explanation
Indices: 391125--391233 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
391115 AGCCGACTCA
*
391125 CCTGTCATCGTTCAAGAGG-CCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCC-CTCCTACCGTTCAAGAGGCC
* **
391167 CCTATCATCCCTCAAGA-GTCCCCTCC-ACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGT-CCCTCCTACCGTTCAAGAGGCC
* *
391208 CCTGTCATTGTTGAAGAGGTCCCTCC
1 CCTGTCATCGTTCAAGAGGTCCCTCC
391234 CAACATTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
41 33 0.60
42 20 0.36
43 2 0.04
ACGTcount: A:0.19, C:0.37, G:0.19, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCCTACCGTTCAAGAGGCC
Found at i:392684 original size:36 final size:30
Alignment explanation
Indices: 392602--392669 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
392592 TAATAAGAGT
392602 TTATTTGTTTAATTGATGTGTAAATAATTC
1 TTATTTGTTTAATTGATGTGTAAATAATTC
392632 TTATTTGTTTAATTGATGTGTAAATAATTC
1 TTATTTGTTTAATTGATGTGTAAATAATTC
392662 TTATTTGT
1 TTATTTGT
392670 GCTTGTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (30 bp):
TTATTTGTTTAATTGATGTGTAAATAATTC
Found at i:392844 original size:20 final size:20
Alignment explanation
Indices: 392819--393102 Score: 274
Period size: 20 Copynumber: 14.8 Consensus size: 20
392809 GCAATTTTCT
392819 CGTTGCGATAGTCAAATTTC-
1 CGTTGCGATAGTCAAA-TTCG
*
392839 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
392859 CGTTACGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
392878 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
392898 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
392918 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
392938 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
392958 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
392972 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
392992 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
393012 CATTGCGAT--T---A-TC-
1 CGTTGCGATAGTCAAATTCG
* * *
393025 CTGTTACGATATTCAAATTCA
1 C-GTTGCGATAGTCAAATTCG
* *
393046 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
393066 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
393086 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
393103 GAATGTGTAA
Statistics
Matches: 220, Mismatches: 28, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
13 1 0.00
14 18 0.08
16 2 0.01
18 2 0.01
19 22 0.10
20 175 0.80
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:392887 original size:59 final size:60
Alignment explanation
Indices: 392812--393099 Score: 246
Period size: 54 Copynumber: 5.0 Consensus size: 60
392802 ACACTTTGCA
*
392812 ATTTTCTCGTTGCGATAGTCAAATTTC-CGTTGCGATAATCAAATTCGCGTTACGATAGTC
1 ATTTTCGCGTTGCGATAGTCAAA-TTCGCGTTGCGATAATCAAATTCGCGTTACGATAGTC
* * *
392872 A-TTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTACGATAGTC
** * * *
392931 ATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TCCCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTACGATAGTC
** ** * *
392985 AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TC-CTGTTACGATATTC
1 ATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGC-GTTACGATAGTC
** ** * * * *
393039 AAATTCATGTTGCGATAGTCATATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTACGATAGTC
393099 A
1 A
393100 AATGAATGTG
Statistics
Matches: 200, Mismatches: 18, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.00
54 95 0.47
55 1 0.00
56 1 0.00
58 4 0.02
59 52 0.26
60 45 0.22
61 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (60 bp):
ATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTACGATAGTC
Found at i:393002 original size:74 final size:74
Alignment explanation
Indices: 392777--393099 Score: 289
Period size: 74 Copynumber: 4.3 Consensus size: 74
392767 CAATCTGCAC
* * * * * * *
392777 CATATTCGCGTTGCGATAGTC-TAATACACTTTGCAATTTTCTCGTTGCGATAGTCAAATTTC-C
1 CATATTCGCGTTGCGATAGTCAT-TTTCGCATTGCGATTATCACGTTGCGATAGTCAAA-TTCGC
*
392840 GTTGCGATAAT
64 GTTGCGATAGT
* * * * *
392851 CAAATTCGCGTTACGATAGTCA-TTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAAT
1 CATATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TCACGTTGCGATAGTCAAAT
392915 TCGCGTTGCGATAGT
60 TCGCGTTGCGATAGT
* *
392930 CATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGT
1 CATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCACGTTGCGATAGTCAAATTCGCGT
392995 TGCGATAGT
66 TGCGATAGT
* * * * * * * * *
393004 CATTTTCGCATTGCGATTA-TCCTGTTACG-ATATTCAAAT-TCATGTTGCGATAGTCATATTCG
1 CATATTCGCGTTGCGA-TAGTCAT-TTTCGCAT-TGCGATTATCACGTTGCGATAGTCAAATTCG
393066 CGTTGCGATAGT
63 CGTTGCGATAGT
393078 CATATTCGCGTTGCGATAGTCA
1 CATATTCGCGTTGCGATAGTCA
393100 AATGAATGTG
Statistics
Matches: 207, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
73 11 0.05
74 120 0.58
75 12 0.06
78 4 0.02
79 47 0.23
80 13 0.06
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (74 bp):
CATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCACGTTGCGATAGTCAAATTCGCGT
TGCGATAGT
Found at i:393299 original size:18 final size:18
Alignment explanation
Indices: 393276--393310 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
393266 AAGCCGGTTG
*
393276 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
393294 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
393311 GCCTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:394507 original size:14 final size:14
Alignment explanation
Indices: 394473--394509 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
394463 TTGCAAACTT
*
394473 ACAAGGAAAACCTC
1 ACAAGGTAAACCTC
394487 ACAAGGTAAACCTC
1 ACAAGGTAAACCTC
394501 ACAAGGTAA
1 ACAAGGTAA
394510 GATGTTTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (14 bp):
ACAAGGTAAACCTC
Found at i:395319 original size:18 final size:18
Alignment explanation
Indices: 395296--395352 Score: 114
Period size: 18 Copynumber: 3.2 Consensus size: 18
395286 TTTTGAAATT
395296 ACTCCCCCTTACTTTAAC
1 ACTCCCCCTTACTTTAAC
395314 ACTCCCCCTTACTTTAAC
1 ACTCCCCCTTACTTTAAC
395332 ACTCCCCCTTACTTTAAC
1 ACTCCCCCTTACTTTAAC
395350 ACT
1 ACT
395353 TCTCATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (18 bp):
ACTCCCCCTTACTTTAAC
Found at i:397715 original size:20 final size:21
Alignment explanation
Indices: 397661--397723 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
397651 GATTCCCCTG
397661 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
397685 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
397705 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
397724 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:398835 original size:42 final size:41
Alignment explanation
Indices: 398783--398932 Score: 115
Period size: 42 Copynumber: 3.6 Consensus size: 41
398773 AAATCATACC
* * *
398783 TTAGCAGCGTTTTATAAACAAACGTCGTAATAGAGTGGTAAT
1 TTAGCGGCGTTTT-TAAACAAACGCCGAAATAGAGTGGTAAT
** * * *
398825 TTAGCGGCGTTTTTAGCTCAAACGCCGCAATTGAGTTGT--T
1 TTAGCGGCGTTTTTA-AACAAACGCCGAAATAGAGTGGTAAT
* * *
398865 TATAGTGGCGTTTTTTCAACAAACACCGAAATAGAGTGGTAAT
1 T-TAGCGGCG-TTTTTAAACAAACGCCGAAATAGAGTGGTAAT
* * **
398908 GTAGCGGCATTTTTGTACAAACGCC
1 TTAGCGGCGTTTTTAAACAAACGCC
398933 ACGATAATGT
Statistics
Matches: 82, Mismatches: 21, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
40 2 0.02
41 39 0.48
42 40 0.49
43 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAAACAAACGCCGAAATAGAGTGGTAAT
Found at i:398898 original size:83 final size:82
Alignment explanation
Indices: 398811--398965 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 82
398801 CAAACGTCGT
* * * *
398811 AATAGAGTGGTAATTTAGCGGCGTTTTTAGCT-CAAACGCCGCAATTGA-GTTGTTTATAGTGGC
1 AATAGAGTGGTAATGTAGCGGCATTTTT-G-TACAAACGCCACAA-TAATGTTGTTTATAGTGGC
*
398874 GTTTTTTCAACAAACACCGA
63 GTTTGTTCAACAAACACCGA
* *
398894 AATAGAGTGGTAATGTAGCGGCATTTTTGTACAAACGCCACGATAATGTTTTTTATAGTGGCGTT
1 AATAGAGTGGTAATGTAGCGGCATTTTTGTACAAACGCCACAATAATGTTGTTTATAGTGGCGTT
398959 TGTTCAA
66 TGTTCAA
398966 AAAATGACGG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
81 3 0.05
82 34 0.54
83 26 0.41
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (82 bp):
AATAGAGTGGTAATGTAGCGGCATTTTTGTACAAACGCCACAATAATGTTGTTTATAGTGGCGTT
TGTTCAACAAACACCGA
Found at i:399084 original size:83 final size:82
Alignment explanation
Indices: 398809--399120 Score: 254
Period size: 83 Copynumber: 3.8 Consensus size: 82
398799 AACAAACGTC
* ** * *
398809 GTAATAGAGTGGTAATTTAGCGGCGTTTTTAGCTCAAACGCCGCAATTG-AGTTGTTTATAGTGG
1 GTAATAGAGTAGTAATTTAGCGGCGTTTTTAAAT-AAACGCCACAATAGTA-TTGTTTATAGTGG
* * ** *
398873 CGTTTTTTCAACAAACACC
64 CGTTTGTTCAAAAAATGCA
* * * * ** * * * * *
398892 GAAATAGAGTGGTAATGTAGCGGCATTTTTGTACAAACGCCACGATAATGTTTTTTATAGTGGCG
1 GTAATAGAGTAGTAATTTAGCGGCGTTTTTAAATAAACGCCACAATAGTATTGTTTATAGTGGCG
*
398957 TTTGTTCAAAAAATGACG
66 TTTGTTCAAAAAATG-CA
* ***
398975 GT-ATAGATTAGTAATTTAGTTACGTTTATTAAATAAACGCCACAATAGTATTGTTTATAGTGGC
1 GTAATAGAGTAGTAATTTAGCGGCGTTT-TTAAATAAACGCCACAATAGTATTGTTTATAGTGGC
*
399039 GTTTGTGCAAAAAATGCA
65 GTTTGTTCAAAAAATGCA
* * * * *
399057 GTAATAGAGTAATAATTTAGCGGCGTTTGTAGGAA-AAACGCCGCAATA-TGTTGTTTATCGTGG
1 GTAATAGAGTAGTAATTTAGCGGCGTTTTTA--AATAAACGCCACAATAGTATTGTTTATAGTGG
399120 C
64 C
399121 ATTTTATAAA
Statistics
Matches: 179, Mismatches: 44, Indels: 13
0.76 0.19 0.06
Matches are distributed among these distances:
82 72 0.40
83 105 0.59
84 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (82 bp):
GTAATAGAGTAGTAATTTAGCGGCGTTTTTAAATAAACGCCACAATAGTATTGTTTATAGTGGCG
TTTGTTCAAAAAATGCA
Found at i:399355 original size:41 final size:41
Alignment explanation
Indices: 399309--399402 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
399299 TTTTGGTAAC
* * * *
399309 AAACGCTGCAAATGGGTCAGACTTTAGTGTCG-TTTTACAAG
1 AAACGCCGCAAA-GGGTCAGACATTAGTGGCGTTTTTACAAA
* *
399350 AAACGCCGTAAAGGGTCATACATTAGTGGCGTTTTTACAAA
1 AAACGCCGCAAAGGGTCAGACATTAGTGGCGTTTTTACAAA
*
399391 AAACACCGCAAA
1 AAACGCCGCAAA
399403 AAAATTATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 16 0.36
41 28 0.64
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (41 bp):
AAACGCCGCAAAGGGTCAGACATTAGTGGCGTTTTTACAAA
Found at i:400333 original size:14 final size:14
Alignment explanation
Indices: 400314--400340 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
400304 TTTATTATTT
400314 CTAGATATATTATA
1 CTAGATATATTATA
400328 CTAGATATATTAT
1 CTAGATATATTAT
400341 GCCATTTCCT
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:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
CTAGATATATTATA
Found at i:404318 original size:21 final size:21
Alignment explanation
Indices: 404300--404361 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
404290 ATGAAGCAAG
404300 GGAAGCAGAAAGAGCAGCAGC
1 GGAAGCAGAAAGAGCAGCAGC
* **
404321 AGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAAAGAGCAGCAGC
* *
404342 GGAAGCAGAGAGAGAAGCAG
1 GGAAGCAGAAAGAGCAGCAG
404362 TGGCAGCACA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.39, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAAAGAGCAGCAGC
Found at i:404369 original size:21 final size:21
Alignment explanation
Indices: 404292--404400 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
404282 AGCGAAAAAT
* *
404292 GAAGCAAG-GGAAGCAGAAAGA
1 GAAGC-AGCGGAAGCACAGAGA
* * *
404313 GCAGCAGCAGAAGCAGC-TAGA
1 GAAGCAGCGGAAGCA-CAGAGA
* *
404334 GCAGCAGCGGAAGCAGAGAGA
1 GAAGCAGCGGAAGCACAGAGA
* *
404355 GAAGCAGTGGCAGCACAGAGA
1 GAAGCAGCGGAAGCACAGAGA
* * *
404376 GAGGCAGCGGTAGAACAGAGA
1 GAAGCAGCGGAAGCACAGAGA
404397 GAAG
1 GAAG
404401 TAATATATCA
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
20 2 0.03
21 67 0.97
ACGTcount: A:0.41, C:0.17, G:0.39, T:0.03
Consensus pattern (21 bp):
GAAGCAGCGGAAGCACAGAGA
Found at i:404853 original size:44 final size:43
Alignment explanation
Indices: 404816--404904 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 43
404806 AAATTTCAAG
* *
404816 ACATATTCTGCGGCGTTTGTAGG-AAAACGCCGTTAAATATCA
1 ACATATTCTACGGCGTTTGTAGGAAAAACGCCGATAAATATCA
* * *
404858 ACATCTTCTACGGCGTTTGTAGGAAAAACGCCGATAAAAATAA
1 ACATATTCTACGGCGTTTGTAGGAAAAACGCCGATAAATATCA
404901 ACAT
1 ACAT
404905 CTACTGCAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 21 0.51
43 20 0.49
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (43 bp):
ACATATTCTACGGCGTTTGTAGGAAAAACGCCGATAAATATCA
Found at i:404963 original size:43 final size:42
Alignment explanation
Indices: 404824--405004 Score: 148
Period size: 43 Copynumber: 4.2 Consensus size: 42
404814 AGACATATTC
* *
404824 TGCGGCGTTTGTAGGAAAACGCCGTTAAATATCAACATCT-T
1 TGCGGCGTTTGTAGGAAAACGCCGATAAAAATCAACATCTAT
* * *
404865 CTACGGCGTTTGTAGGAAAAACGCCGATAAAAATAAACATCTAC
1 -TGCGGCGTTTGTAGG-AAAACGCCGATAAAAATCAACATCTAT
* * * * * *
404909 TGCAGCATTTGTGAAGAAAACGCCGCTAAACATCAACGTCTAT
1 TGCGGCGTTTGT-AGGAAAACGCCGATAAAAATCAACATCTAT
* ** * * * *
404952 TGCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAACACCTAT
1 TGCGGCGTTTGT-AGGAAAACGCCGATAAAAATCAACATCTAT
*
404995 TACGGCGTTT
1 TGCGGCGTTT
405005 TTCTACCAAA
Statistics
Matches: 109, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
42 14 0.13
43 93 0.85
44 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
TGCGGCGTTTGTAGGAAAACGCCGATAAAAATCAACATCTAT
Found at i:405014 original size:43 final size:43
Alignment explanation
Indices: 404926--405035 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 43
404916 TTTGTGAAGA
* ** * *
404926 AAACGCCGCTAAACATCAACGTCTATTGCGGCGTTTGTCTGCC
1 AAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTCTACC
* * *
404969 AAATGCCGTTAAATATCAACACCTATTACGGCGTTTTTCTACC
1 AAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTCTACC
*
405012 AAACGCCGCTAAATATCAATACCT
1 AAACGCCGCTAAATATCAACACCT
405036 TTTGTGGCGA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTCTACC
Found at i:408125 original size:20 final size:20
Alignment explanation
Indices: 408083--408125 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
408073 TTGTTTTCAT
* *
408083 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
408103 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
408123 TTT
1 TTT
408126 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:411798 original size:24 final size:24
Alignment explanation
Indices: 411771--411836 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
411761 CAAAATCTGA
411771 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTCCGG
411795 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTCCGG
411819 GTATTGACCAAGATCAAA
1 GTATTGACCAAGATCAAA
411837 TTTCGAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTCCGG
Found at i:412683 original size:20 final size:20
Alignment explanation
Indices: 412655--412761 Score: 135
Period size: 20 Copynumber: 5.3 Consensus size: 20
412645 AATTCAGTGA
*
412655 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
412675 TGCGATAGTCACAATCGCAT
1 TGCGATAGTCAGAATCGCGT
**
412695 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
*
412716 TGCGATAGTCCGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
412736 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
412756 TGCGAT
1 TGCGAT
412762 CACATGTTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.76
21 14 0.19
22 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:412725 original size:61 final size:61
Alignment explanation
Indices: 412655--412782 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
412645 AATTCAGTGA
* * *
412655 TGCGTTAGTCAGAATCGCGTTGCGATAGTCACAATCGCATTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCACAATCGCATTGCGATCACATATTATCACGT
* * * *
412716 TGCGATAGTCCGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACATGTTATCACGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCACAATCGCATTGCGATCACATATTATCACGT
412777 TGCGAT
1 TGCGAT
412783 TTACATATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCACAATCGCATTGCGATCACATATTATCACGT
Found at i:412801 original size:20 final size:20
Alignment explanation
Indices: 412776--412823 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
412766 TGTTATCACG
412776 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
412796 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
412816 TTGCGATT
1 TTGCGATT
412824 ATCTAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:423133 original size:22 final size:21
Alignment explanation
Indices: 423115--423183 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 21
423105 TATTATTTCA
423115 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* *
423135 AATTAATTGAAATTAAATATTT
1 AATTAATT-AAAATATATATTT
*
423157 AGATT-ATTAAAACATATATTT
1 A-ATTAATTAAAATATATATTT
423178 AATTAA
1 AATTAA
423184 CTCTAGATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.28
21 12 0.30
22 14 0.35
23 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:423133 original size:90 final size:89
Alignment explanation
Indices: 422988--423153 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 89
422978 CTTTTATAGT
*
422988 CAAGTTACCCTAATTATATTAGGATTTTATTATTTCAAATTAATTAAATATATATTTAATTAATT
1 CAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATATTTAATTAATT
*
423053 GAAATTTAATAATCCTCTTATATC
66 GAAATTAAATAATCCTCTTATATC
*
423077 CAAGTTATCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATATATTTAATTAAT
1 CAAGTTACCCTAATCATATTA-GGATTTTATTATTTCAAATTAATTAAATATATATTTAATTAAT
423142 TGAAATTAAATA
65 TGAAATTAAATA
423154 TTTAGATTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 19 0.26
90 54 0.74
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (89 bp):
CAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATATTTAATTAATT
GAAATTAAATAATCCTCTTATATC
Found at i:429822 original size:18 final size:18
Alignment explanation
Indices: 429795--429842 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
429785 CTTGTCTGCC
429795 TATTAATGATTCTGCTCA
1 TATTAATGATTCTGCTCA
* * **
429813 TATTAGTGATTATGCTTG
1 TATTAATGATTCTGCTCA
429831 TATTAATGATTC
1 TATTAATGATTC
429843 CTCTCATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (18 bp):
TATTAATGATTCTGCTCA
Found at i:432113 original size:40 final size:40
Alignment explanation
Indices: 432058--432138 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
432048 ATTTATGATT
*
432058 TGTTAAAAAGGTCAAACCTAGATGAGTCAACACCTACACA
1 TGTTAAAAAGATCAAACCTAGATGAGTCAACACCTACACA
432098 TGTTAAAAAGATCAAACCTAGATGAGTCAACACCTACACA
1 TGTTAAAAAGATCAAACCTAGATGAGTCAACACCTACACA
432138 T
1 T
432139 ACTCCTATGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (40 bp):
TGTTAAAAAGATCAAACCTAGATGAGTCAACACCTACACA
Found at i:432918 original size:25 final size:24
Alignment explanation
Indices: 432889--432961 Score: 110
Period size: 25 Copynumber: 3.0 Consensus size: 24
432879 CAGTCATGAG
* *
432889 AAGCAGATTTGAGCTGCCATGAAAT
1 AAGCAGTTTTGAGTTGCCA-GAAAT
432914 AAGCAGTTTTGAGTTGCCAGGAAAT
1 AAGCAGTTTTGAGTTGCCA-GAAAT
432939 AAGCAGTTTTGAGTTGCCAGAAA
1 AAGCAGTTTTGAGTTGCCAGAAA
432962 AATGTTGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 4 0.09
25 41 0.91
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (24 bp):
AAGCAGTTTTGAGTTGCCAGAAAT
Found at i:438560 original size:30 final size:30
Alignment explanation
Indices: 438524--438584 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
438514 TTCATGGGTG
438524 ACTCTCCAGGGCTCTTACGAACTGAAACAC
1 ACTCTCCAGGGCTCTTACGAACTGAAACAC
438554 ACTCTCCAGGGCTCTTACGAACTGAAACAC
1 ACTCTCCAGGGCTCTTACGAACTGAAACAC
438584 A
1 A
438585 TGAACCCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (30 bp):
ACTCTCCAGGGCTCTTACGAACTGAAACAC
Found at i:441778 original size:60 final size:59
Alignment explanation
Indices: 441603--441780 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 59
441593 TTACGTATCT
* * ** *
441603 GGATGAAATTGGAATATTCAAAAGTTTGGGGACCAATTTAGAAAGATTG-TTATATTTTAG
1 GGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTA-AAAGA-TGATTATAGTTTAG
* ** *
441663 GGATGAAAATATAATATTCAAAAGTTTAAGGATTAATTTAGAACGA-GATTCATAGTTTAG
1 GGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTA-AAAGATGATT-ATAGTTTAG
* *
441723 GGATGAAACTAGAATATTCAAAAGTTTAAGGAGCAATTTAAAATGATGATTATAGTTT
1 GGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTAAAA-GATGATTATAGTTT
441781 GGAGACATAT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.01
59 4 0.04
60 91 0.91
61 4 0.04
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (59 bp):
GGATGAAAATAGAATATTCAAAAGTTTAAGGACCAATTTAAAAGATGATTATAGTTTAG
Found at i:442510 original size:2 final size:2
Alignment explanation
Indices: 442501--442552 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
442491 TTTTTTCATG
442501 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
442542 TA TA TA T- TA TA
1 TA TA TA TA TA TA
442553 CATAGTCGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:443766 original size:34 final size:34
Alignment explanation
Indices: 443723--443794 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
443713 ATGAATCTTC
*
443723 TTTTTACTGTATGACCTAATTACAATGTAATTTA
1 TTTTTACTGTATGACATAATTACAATGTAATTTA
*
443757 TTTTTACTGTATGAGATAATTACAATGTAATTTA
1 TTTTTACTGTATGACATAATTACAATGTAATTTA
443791 TTTT
1 TTTT
443795 CTCTTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (34 bp):
TTTTTACTGTATGACATAATTACAATGTAATTTA
Found at i:444811 original size:59 final size:59
Alignment explanation
Indices: 444677--444821 Score: 145
Period size: 59 Copynumber: 2.4 Consensus size: 59
444667 AACGTAATAA
* * *
444677 ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGCAACTCCAT
1 ATAGTCGGG-GACCATTTTGTAACTTTGAATAGTCGAGGGACTCAACAAAGCAACTCCAT
* * * *
444737 ATAGTTGGGGGCCATTTTGTAACTTTGAATAGTCG-GGGAACTCAATAAAGTAGTA-TCC-T
1 ATAGTCGGGGACCATTTTGTAACTTTGAATAGTCGAGGG-ACTCAACAAAGCA--ACTCCAT
*
444796 ATAGTCGTGGACCATTTGTGT-ACTTT
1 ATAGTCGGGGACCATTT-TGTAACTTT
444822 ACCCTATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
58 3 0.04
59 53 0.75
60 14 0.20
61 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (59 bp):
ATAGTCGGGGACCATTTTGTAACTTTGAATAGTCGAGGGACTCAACAAAGCAACTCCAT
Found at i:458542 original size:134 final size:134
Alignment explanation
Indices: 458297--459456 Score: 1445
Period size: 134 Copynumber: 8.7 Consensus size: 134
458287 GAAATATAAT
* * * * *
458297 GAGGGATCTGTTCTGTTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCTACTGC
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
* * * * ** *
458362 CACTCAGGGAAGATTAAATTGAGGTAGACTTGTTCCACTGTTACTCATAGAAAATCAAATCTTGA
66 CACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGA
458427 AAGA
131 AAGA
* * * * *
458431 GGGGGATCTGTTCCGCTTTTTCTTGAGGAAAAATTAGATATGGGGAAGTTGATTCATTCCACTAT
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
* *
458496 CACTCAGGGAAGATTGAATCAAGGAAGACTTGTTTCACTGTCACTCAGGGAATATCAAATCTTGA
66 CACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGA
*
458561 AAAA
131 AAGA
* * * * * * *
458565 GTGGGATTTGTTCTGCTTCTTCATGAGGGAAAATTAGATATTGGGG-AGTTGATCCATTCCACTC
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATA-TGGGGAAGTTGATTCATTCCACTG
* * * *
458629 TCACTTAAGGAAGATTGAATTGA-GACAGATTTGTTCCACTGTCACTCAGGGAATATCAAATCTT
65 TCACTCAGGGAAGATTGAATCGAGGA-AGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTT
458693 GAAAGA
129 GAAAGA
* * * * *
458699 GAGGGATCTATTCAGCTTCTTCTTGAGGGAAAATCAGATCTTGGGG-AGTTGATCCATTCTACTG
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGAT-ATGGGGAAGTTGATTCATTCCACTG
* * * * *
458763 TCACTCAGGAAAGATTGAATCGA-GACAGACTTATTCCACTATTACTCAGGGAAAATCAAATCTT
65 TCACTCAGGGAAGATTGAATCGAGGA-AGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTT
458827 GAAAGA
129 GAAAGA
* * ** *
458833 GATGGATCTGGTCTACTTCTTCTTGAGGGAAAAATTAGATATGGGGAAGTTGATTCATTCCACTG
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGG-AAAATCAGATATGGGGAAGTTGATTCATTCCACTG
* *
458898 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAAGCTTG
65 TCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
458963 AAAGA
130 AAAGA
* * ** * * *
458968 GAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCT-ACGAGAGTTGATACATTCTATTG
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGA-AGTTGATTCATTCCACTG
* * * * *
459032 TCACTTAGGGAAGATTGAATCGAGGCAGACTTGTTTCACTATCAC-CTAGGGAATATAAAATCTT
65 TCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTC-AGGGAATATCAAATCTT
459096 GAAAGA
129 GAAAGA
* * * *
459102 GAGAGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTTGGGG-AGTTG-TTCATTCCACTA
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGAT-ATGGGGAAGTTGATTCATTCCACTG
* * *
459165 TCACTAAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTG
65 TCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
459230 AAAGA
130 AAAGA
* * ** * * * *
459235 GAGGGATTTTTTTAGCTTTTTCTTCAGGGAAAATCATATATGGGGATGTTGATTCATTCCACTGT
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
* * *
459300 CACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAGGAATATAAAATCTTGA
66 CACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGA
459365 AAGA
131 AAGA
* * * * *
459369 GAAGGATATGTTCCGCTTCTGCTTGAGGGAAAATCAAATATGGGGATGTTGATTCATTCCACTGT
1 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
459434 CACTCAGGGAAGATTGAATCGAG
66 CACTCAGGGAAGATTGAATCGAG
459457 TTTGATTCGT
Statistics
Matches: 888, Mismatches: 125, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
132 5 0.01
133 110 0.12
134 655 0.74
135 116 0.13
136 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (134 bp):
GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAAGTTGATTCATTCCACTGT
CACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGA
AAGA
Found at i:459046 original size:403 final size:402
Alignment explanation
Indices: 458297--459456 Score: 1621
Period size: 403 Copynumber: 2.9 Consensus size: 402
458287 GAAATATAAT
* * *
458297 GAGGGATCTGTTCTGTTTCTTCTTGAGGGAAAATCAGAT-ATGGGGACGTTGATTCATTCTACTG
1 GAGGGATCTGTTCAGCTTCTTCTTGAGGGAAAATCAGATCTTGGGGA-GTTGATTCATTCTACTG
* * * **
458361 CCACTCAGGGAAGATTAAATTGAGGTAGACTTGTTCCACTGTTACTCATAGAAAATCAAATCTTG
65 TCACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAAAATCAAATCTTG
* **
458426 AAAGAGGGGGATCTGTTCCGCTTTTTCTTGA-GGAAAAATTAGATATGGGGAAGTTGATTCATTC
130 AAAGAGAGGGATCTGTTCTACTTTTTCTTGAGGGAAAAATTAGATATGGGGAAGTTGATTCATTC
* * *
458490 CACTATCACTCAGGGAAGATTGAATCAAGGAAGACTTGTTTCACTGTCACTCAGGGAATATCAAA
195 CACTGTCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAA
* * * * * *
458555 TCTTGAAAAAGTGGGATTTGTTCTGCTTCTTCATGAGGGAAAATTAGATATTGGGGAGTTGATCC
260 TCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAGATA-TGGGGAGTTGATAC
* * * * *
458620 ATTCCACTCTCACTTAAGGAAGATTGAATTGAGACAGATTTGTTCCACTGTCA-CTCAGGGAATA
324 ATTCCACTGTCACTTAGGGAAGATTGAATCGAGACAGACTTGTTCCACTATCACCT-AGGGAATA
*
458684 TCAAATCTTGAAAGA
388 TAAAATCTTGAAAGA
* *
458699 GAGGGATCTATTCAGCTTCTTCTTGAGGGAAAATCAGATCTTGGGGAGTTGATCCATTCTACTGT
1 GAGGGATCTGTTCAGCTTCTTCTTGAGGGAAAATCAGATCTTGGGGAGTTGATTCATTCTACTGT
* ** * *
458764 CACTCAGGAAAGATTGAATCGAGACAGACTTATTCCACTATTACTCAGGGAAAATCAAATCTTGA
66 CACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAAAATCAAATCTTGA
* * *
458829 AAGAGATGGATCTGGTCTACTTCTTCTTGAGGGAAAAATTAGATATGGGGAAGTTGATTCATTCC
131 AAGAGAGGGATCTGTTCTACTTTTTCTTGAGGGAAAAATTAGATATGGGGAAGTTGATTCATTCC
* *
458894 ACTGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAAG
196 ACTGTCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAAT
* * *
458959 CTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTACGAGAGTTGATACA
261 CTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAGATAT-GGGGAGTTGATACA
* * * *
459024 TTCTATTGTCACTTAGGGAAGATTGAATCGAGGCAGACTTGTTTCACTATCACCTAGGGAATATA
325 TTCCACTGTCACTTAGGGAAGATTGAATCGAGACAGACTTGTTCCACTATCACCTAGGGAATATA
459089 AAATCTTGAAAGA
390 AAATCTTGAAAGA
* * * * *
459102 GAGAGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTTGGGGAGTTG-TTCATTCCACTAT
1 GAGGGATCTGTTCAGCTTCTTCTTGAGGGAAAATCAGATCTTGGGGAGTTGATTCATTCTACTGT
* *
459166 CACTAAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
66 CACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAAAATCAAATCTTGA
* * * * * *
459231 AAGAGAGGGAT-TTTTTTAGCTTTTTCTTCAGGG-AAAATCATATATGGGGATGTTGATTCATTC
131 AAGAGAGGGATCTGTTCTA-CTTTTTCTTGAGGGAAAAATTAGATATGGGGAAGTTGATTCATTC
* * *
459294 CACTGTCACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAGGAATATAAAA
195 CACTGTCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAA
* * * * *
459359 TCTTGAAAGAGAAGGATATGTTCCGCTTCTGCTTGAGGGAAAATCAAATATGGGGATGTTGATTC
260 TCTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGA-GTTGATAC
*
459424 ATTCCACTGTCACTCAGGGAAGATTGAATCGAG
324 ATTCCACTGTCACTTAGGGAAGATTGAATCGAG
459457 TTTGATTCGT
Statistics
Matches: 669, Mismatches: 83, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
400 3 0.00
401 175 0.26
402 223 0.33
403 266 0.40
404 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (402 bp):
GAGGGATCTGTTCAGCTTCTTCTTGAGGGAAAATCAGATCTTGGGGAGTTGATTCATTCTACTGT
CACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAAAATCAAATCTTGA
AAGAGAGGGATCTGTTCTACTTTTTCTTGAGGGAAAAATTAGATATGGGGAAGTTGATTCATTCC
ACTGTCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTCACTCAGGGAATATCAAAT
CTTGAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGAGTTGATACAT
TCCACTGTCACTTAGGGAAGATTGAATCGAGACAGACTTGTTCCACTATCACCTAGGGAATATAA
AATCTTGAAAGA
Found at i:463880 original size:20 final size:19
Alignment explanation
Indices: 463855--463894 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
463845 TATGACTAAT
463855 TTATGCCTACTTGCTAAGGA
1 TTATG-CTACTTGCTAAGGA
**
463875 TTATGCTTGTTGCTAAGGA
1 TTATGCTACTTGCTAAGGA
463894 T
1 T
463895 GAGCATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (19 bp):
TTATGCTACTTGCTAAGGA
Found at i:466890 original size:21 final size:22
Alignment explanation
Indices: 466845--466896 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
466835 CACCTAACAA
* * *
466845 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACATCCATGAAGG
466867 TGCATCGATACA-CCATGAAGG
1 TGCATCGATACATCCATGAAGG
*
466888 TGCACCGAT
1 TGCATCGAT
466897 GCACGCCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATACATCCATGAAGG
Found at i:466919 original size:23 final size:23
Alignment explanation
Indices: 466845--466924 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
466835 CACCTAACAA
*
466845 TGCATCGATGCA-TCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
* *
466867 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
466888 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
*
466911 TGTATCGATGCACA
1 TGCATCGATGCACA
466925 AGGTCATGCA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 9 0.20
23 20 0.44
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:466940 original size:43 final size:41
Alignment explanation
Indices: 466843--466942 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 41
466833 TACACCTAAC
* * *
466843 AATGCATCGATGCATCCTTGAATGTGCATCGATACACCATG
1 AATGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGG
* * *
466884 AAGGTGCACCGATGCACGCCTTGAATGTGTATCGATGCACAAGG
1 AA--TGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG
*
466928 TCATGCATCGATGCA
1 -AATGCATCGATGCA
466943 TCAGTCAGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
43 22 0.47
44 22 0.47
45 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (41 bp):
AATGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGG
Found at i:467373 original size:13 final size:13
Alignment explanation
Indices: 467355--467379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
467345 AATTCAAAAA
467355 TCTAAATTTGATT
1 TCTAAATTTGATT
467368 TCTAAATTTGAT
1 TCTAAATTTGAT
467380 GTTTTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TCTAAATTTGATT
Found at i:469695 original size:65 final size:64
Alignment explanation
Indices: 469609--469759 Score: 173
Period size: 65 Copynumber: 2.3 Consensus size: 64
469599 GAATAAATTG
* * * *
469609 AACATAGAATGAATTTCATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAG-T-TTTAT
1 AACATCGAATGCATTTCATGCACCGATGCACCA-ACCATGCATAGATGCACTCAG-GCTATTT-T
469671 GAA
63 G-A
* * *
469674 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATAGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCACCGATGCACCAACCATGCATAGATGCACTCAGGCTATTTTGA
*
469738 AACATCGAATGCATTTTATGCA
1 AACATCGAATGCATTTCATGCA
469760 TTGCACTCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 23 0.31
65 47 0.63
66 5 0.07
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCACCGATGCACCAACCATGCATAGATGCACTCAGGCTATTTTGA
Found at i:474786 original size:16 final size:16
Alignment explanation
Indices: 474761--474840 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
474751 CCCATTTCAA
* *
474761 TTTTCCTTATTCTCTT
1 TTTTCTTTATTCTTTT
* *
474777 TTTTATTTATCCTTTCT
1 TTTTCTTTATTCTTT-T
*
474794 TTTTCTTTTTTCTTTT
1 TTTTCTTTATTCTTTT
474810 TTTTCTTT-TTCTTTT
1 TTTTCTTTATTCTTTT
*
474825 TTTCCCTTTATT-TTTT
1 TTT-TCTTTATTCTTTT
474841 AGTGTGGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
15 10 0.19
16 28 0.53
17 15 0.28
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTATTCTTTT
Found at i:474800 original size:6 final size:6
Alignment explanation
Indices: 474789--474825 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
474779 TTATTTATCC
*
474789 TTTCTT TTTCTT TTT-TC TTT-TT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
474826 TTCCCTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.29
6 20 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTCTT
Found at i:474802 original size:22 final size:22
Alignment explanation
Indices: 474784--474826 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
474774 CTTTTTTATT
474784 TATCCTTTCTTTTTCTTTTTTC
1 TATCCTTTCTTTTTCTTTTTTC
* **
474806 TTTTTTTTCTTTTTCTTTTTT
1 TATCCTTTCTTTTTCTTTTTT
474827 TCCCTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (22 bp):
TATCCTTTCTTTTTCTTTTTTC
Found at i:474841 original size:7 final size:7
Alignment explanation
Indices: 474789--474826 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
474779 TTATTTATCC
474789 TTTC-TT
1 TTTCTTT
474795 TTTCTTT
1 TTTCTTT
474802 TTTCTTT
1 TTTCTTT
*
474809 TTTTTCTT
1 TTTCT-TT
474817 TTTCTTT
1 TTTCTTT
474824 TTT
1 TTT
474827 TCCCTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 4 0.14
7 18 0.64
8 6 0.21
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTCTTT
Found at i:477192 original size:24 final size:24
Alignment explanation
Indices: 477165--477213 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
477155 TGTATGACAT
477165 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
477189 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
477213 T
1 T
477214 CAGAAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:478939 original size:19 final size:19
Alignment explanation
Indices: 478905--478963 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 19
478895 AAGAATACTA
478905 ATAATAGAAGTGTAAAAAATG
1 ATAA-AGAA-TGTAAAAAATG
*
478926 ATAAAGAATGTAAAGAATG
1 ATAAAGAATGTAAAAAATG
* *
478945 -TGAA-AATGTATAAAATG
1 ATAAAGAATGTAAAAAATG
478962 AT
1 AT
478964 TGCCACTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 11 0.33
18 4 0.12
19 10 0.30
20 4 0.12
21 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (19 bp):
ATAAAGAATGTAAAAAATG
Found at i:485200 original size:15 final size:15
Alignment explanation
Indices: 485180--485215 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
485170 AAATGTATTT
485180 ATATTAATAATAATA
1 ATATTAATAATAATA
485195 ATATTAATAATAATA
1 ATATTAATAATAATA
485210 ATATTA
1 ATATTA
485216 TTATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:487088 original size:20 final size:20
Alignment explanation
Indices: 487030--487088 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
487020 GCCACTTTTT
487030 CTTTATTTCTTTGCACTTTATCA
1 CTTTATTTCTTT--A-TTTATCA
* *
487053 CTTT-GTTCTATAATTTATCA
1 CTTTATTTCT-TTATTTATCA
487073 CTTTATTTCTTTATTT
1 CTTTATTTCTTTATTT
487089 TTTTTTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 16 0.53
21 5 0.17
22 4 0.13
23 5 0.17
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.61
Consensus pattern (20 bp):
CTTTATTTCTTTATTTATCA
Found at i:487926 original size:60 final size:58
Alignment explanation
Indices: 487844--487962 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 58
487834 AATAATGATC
487844 TTCATTTAAATTAGTCCTCAAAC-TTTTAAATATTTCAATTTCATCTTCAAACTATGACA
1 TTCATTTAAATTAGTCCTCAAACTTTTTAAATATTTCAATTTCATC-TCAAACTAT-ACA
*
487903 TTCATTCTAAATTAGTGCC-CAAACTTTTTGAATATTTCAATTTCATCTCAAACTATACA
1 TTCATT-TAAATTAGT-CCTCAAACTTTTTAAATATTTCAATTTCATCTCAAACTATACA
487962 T
1 T
487963 ATATACCAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
59 10 0.18
60 23 0.41
61 23 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (58 bp):
TTCATTTAAATTAGTCCTCAAACTTTTTAAATATTTCAATTTCATCTCAAACTATACA
Found at i:488562 original size:2 final size:2
Alignment explanation
Indices: 488555--488579 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
488545 GATCAAGCTG
488555 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
488580 GTACAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:497886 original size:15 final size:15
Alignment explanation
Indices: 497821--497887 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
497811 CGACTAAAAA
*
497821 TATTATTATTCT-AT
1 TATTATTATTATAAT
497835 TATTA-T-TTATAAT
1 TATTATTATTATAAT
* *
497848 AAATATTATTATAAT
1 TATTATTATTATAAT
*
497863 TGTTATTATTATTAAT
1 TATTATTATTA-TAAT
497879 TATT-TTATT
1 TATTATTATT
497888 TACACATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.07
13 6 0.14
14 6 0.14
15 20 0.48
16 7 0.17
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (15 bp):
TATTATTATTATAAT
Found at i:499440 original size:30 final size:30
Alignment explanation
Indices: 499355--499469 Score: 117
Period size: 30 Copynumber: 3.8 Consensus size: 30
499345 TTTAAGATTT
*
499355 TATTTTTACTATTTT-AGTCCTTTAAATATC
1 TATTTTTACTATTTTGA-TCCTTTAAATGTC
* * *
499385 TATTTTTGCTATTTTAATCCCTTAAATGTC
1 TATTTTTACTATTTTGATCCTTTAAATGTC
*
499415 TATTTTTACTATTTTGGAT-CTTTAAATGTT
1 TATTTTTACTATTTT-GATCCTTTAAATGTC
* ** *
499445 TGTTTTTGTTTTTTTGATCCTTTAA
1 TATTTTTACTATTTTGATCCTTTAA
499470 GTTTCTTTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
29 3 0.04
30 65 0.92
31 3 0.04
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (30 bp):
TATTTTTACTATTTTGATCCTTTAAATGTC
Found at i:503152 original size:19 final size:19
Alignment explanation
Indices: 503122--503218 Score: 75
Period size: 15 Copynumber: 5.3 Consensus size: 19
503112 AAATAAACAG
503122 CAAAGAAGCAAAGGAAAAAA
1 CAAAG-AGCAAAGGAAAAAA
*
503142 CAAAGAGCAAA-G-AGAAA
1 CAAAGAGCAAAGGAAAAAA
*
503159 C-AA-AGCAAA--AAAAGA
1 CAAAGAGCAAAGGAAAAAA
*
503174 -AAA-AGCAAAGAAAAAAA
1 CAAAGAGCAAAGGAAAAAA
503191 CAAAGAGCAAAGAAGAAAAAA
1 CAAAGAGCAAAG--GAAAAAA
503212 TCAAAGA
1 -CAAAGA
503219 AAAGAACAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
15 17 0.27
16 2 0.03
17 10 0.16
18 4 0.06
19 13 0.21
20 5 0.08
21 6 0.10
22 6 0.10
ACGTcount: A:0.71, C:0.10, G:0.18, T:0.01
Consensus pattern (19 bp):
CAAAGAGCAAAGGAAAAAA
Found at i:503182 original size:49 final size:50
Alignment explanation
Indices: 503127--503224 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 50
503117 AACAGCAAAG
*
503127 AAGCAAAGGAAAAAACAAAGAGCAAAG-AGAAACAAAGCAAA-AAAAGAAA
1 AAGCAAAGAAAAAAACAAAGAGCAAAGAAGAAA-AAAGCAAAGAAAAGAAA
*
503176 AAGCAAAGAAAAAAACAAAGAGCAAAGAAGAAAAAATCAAAGAAAAGAA
1 AAGCAAAGAAAAAAACAAAGAGCAAAGAAGAAAAAAGCAAAGAAAAGAA
503225 CAAAATAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 33 0.73
50 12 0.27
ACGTcount: A:0.72, C:0.09, G:0.17, T:0.01
Consensus pattern (50 bp):
AAGCAAAGAAAAAAACAAAGAGCAAAGAAGAAAAAAGCAAAGAAAAGAAA
Found at i:503222 original size:20 final size:21
Alignment explanation
Indices: 503181--503239 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
503171 AGAAAAAGCA
503181 AAGAAAAAAACAAAGAGCAAAG
1 AAGAAAAAAACAAAGA-CAAAG
*
503203 AAGAAAAAATCAAAGA-AAAG
1 AAGAAAAAAACAAAGACAAAG
* *
503223 AACAAAATAAAGAAAGA
1 AAGAAAA-AAACAAAGA
503240 ATACAAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 10 0.31
21 7 0.22
22 15 0.47
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (21 bp):
AAGAAAAAAACAAAGACAAAG
Found at i:503234 original size:17 final size:17
Alignment explanation
Indices: 503154--503237 Score: 61
Period size: 17 Copynumber: 5.0 Consensus size: 17
503144 AAGAGCAAAG
*
503154 AGAAACAAAGCAAA-AAA
1 AGAAA-AAATCAAAGAAA
*
503171 AG-AAAAAGCAAAGAAA
1 AGAAAAAATCAAAGAAA
* *
503187 AAAACAAAGAGCAAAG--A
1 AGAA-AAA-ATCAAAGAAA
503204 AGAAAAAATCAAAGAAA
1 AGAAAAAATCAAAGAAA
503221 AGAACAAAAT-AAAGAAA
1 AGAA-AAAATCAAAGAAA
503238 GAATACAAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
15 14 0.25
16 9 0.16
17 19 0.33
18 8 0.14
19 7 0.12
ACGTcount: A:0.75, C:0.08, G:0.14, T:0.02
Consensus pattern (17 bp):
AGAAAAAATCAAAGAAA
Found at i:504236 original size:343 final size:339
Alignment explanation
Indices: 503609--504283 Score: 1161
Period size: 343 Copynumber: 2.0 Consensus size: 339
503599 AGTAGTACCG
*
503609 ATAATGTTCTTTGCAGTATCAATACCAGTCCTTACATGTAGTATCAATACCTTAGACAAAGGTAG
1 ATAATGTTCTTTGCAGTATCAATACCACTCCTTACATGTAGTATCAATACCTTAGACAAAGGTAG
*
503674 TACCGATACCATCAAGGTAGTATTGATACTACCATAAAGGCTCAAAACATCGAATACAAAATGGG
66 TACCGATACCATCAAGGTAGTACTGATACTACCATAAAGGCTCAAAACATCGAATACAAAATGGG
503739 TATACCATGCAAGGGTATCGATACCATAGTGCAAAGTAGTACCGATACCCCTTAGGAAGTATCGA
131 TATACCATGCAAGGGTATCGATACCATAGTGCAAAGTAGTACCGATACCCCTTAGGAAGTATCGA
* *
503804 TACTACAAGGCTCCAACTACTAGCAACGACTACTTAAATTAGAATTTAACAAAGTTAGTACCGAT
196 TAATACAAGGCTCCAACCACTAGCAACGACTACTTAAATTAGAATTTAACAAAGTTAGTACCGAT
* * *
503869 ACCCCATATTGGAGTACTAATACTTCTAGTTCTGGACAACCTTATTTTGTAGAAAATTAATCCCC
261 ACCCCATAGTGGAGTACCAATACTTCTAGTTCTGGACAACCTTATTTTATAGAAAATTAATCCCC
503934 AACGGCTCCAAAAC
326 AACGGCTCCAAAAC
* *
503948 ATAATGTTCTTTGCAGTATCGATACCACTCCTTACATGTAGTATCGATACCTTAGACAAAGGTAG
1 ATAATGTTCTTTGCAGTATCAATACCACTCCTTACATGTAGTATCAATACCTTAGACAAAGGTAG
* * *
504013 TACCGATACCATTAAGGTAGTACTGATACTACTATAAAGGCTCAAAACATCGAATGCAAAATGGG
66 TACCGATACCATCAAGGTAGTACTGATACTACCATAAAGGCTCAAAACATCGAATACAAAATGGG
*
504078 TACCAATACCATGCAAGGGTATCGATACCATAGTGCAAAGTAGTACTGATACCCCTTAGGAAGTA
131 T----ATACCATGCAAGGGTATCGATACCATAGTGCAAAGTAGTACCGATACCCCTTAGGAAGTA
* * *
504143 TCGATAATATAAGGCTCCAACCGCTAGCAACGACTACTTAAATTTGAATTTAACAAAGTTAGTAC
192 TCGATAATACAAGGCTCCAACCACTAGCAACGACTACTTAAATTAGAATTTAACAAAGTTAGTAC
504208 CGATACCCCATAGTGGAGTACCAATACTTCTAGTTCTGGACAACCTTATTTTATAGAAAATTAAT
257 CGATACCCCATAGTGGAGTACCAATACTTCTAGTTCTGGACAACCTTATTTTATAGAAAATTAAT
*
504273 CCCCTACGGCT
322 CCCCAACGGCT
504284 ATATACGACT
Statistics
Matches: 315, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
339 124 0.39
343 191 0.61
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (339 bp):
ATAATGTTCTTTGCAGTATCAATACCACTCCTTACATGTAGTATCAATACCTTAGACAAAGGTAG
TACCGATACCATCAAGGTAGTACTGATACTACCATAAAGGCTCAAAACATCGAATACAAAATGGG
TATACCATGCAAGGGTATCGATACCATAGTGCAAAGTAGTACCGATACCCCTTAGGAAGTATCGA
TAATACAAGGCTCCAACCACTAGCAACGACTACTTAAATTAGAATTTAACAAAGTTAGTACCGAT
ACCCCATAGTGGAGTACCAATACTTCTAGTTCTGGACAACCTTATTTTATAGAAAATTAATCCCC
AACGGCTCCAAAAC
Found at i:508026 original size:33 final size:33
Alignment explanation
Indices: 507973--508036 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
507963 AAGGGGTTTT
* *
507973 GGTTCTAGCTAAGCCTGTGAAAAGCTAGGGAAA
1 GGTTCTAGCTAAGCCCGTGAAAAACTAGGGAAA
* *
508006 GGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 GGTTCTAGCTAAGCCCGTGAAAAACTAGGGA
508037 GTTTGTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (33 bp):
GGTTCTAGCTAAGCCCGTGAAAAACTAGGGAAA
Found at i:508111 original size:19 final size:19
Alignment explanation
Indices: 508087--508124 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
508077 CAAATTAGTA
508087 AATTTGTTGGAAAATCCTT
1 AATTTGTTGGAAAATCCTT
508106 AATTTGTTGGAAAATCCTT
1 AATTTGTTGGAAAATCCTT
508125 TGGTGAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
AATTTGTTGGAAAATCCTT
Found at i:512927 original size:64 final size:63
Alignment explanation
Indices: 512657--512945 Score: 225
Period size: 64 Copynumber: 4.5 Consensus size: 63
512647 GGTATTTCCC
* * * *
512657 TTGAAACAAATTTTG--TCTCTTGAGACAGTTTCTTTTGTAAAAAAAATCTTTGTG-TAAGTTTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAG-TT-TTTT-TAAGAAAAACCTTTGAGAT-TGTTTC
512719 T-
62 TA
* * * * * * * **
512720 TTGGAAACAAAGTTTTGTCTCTCTTGATACAATTTCCTTTGAGAAAAAAACATTGATATCATTTC
1 TT-GAAACAAA-TTTTGTCTCTCTTGAGACAGTTT-TTTTAAG-AAAAACCTTTGAGATTGTTTC
512785 TA
62 TA
* * *
512787 TTGAAACAAATTTTG--TCTCTTGAGATAGTTTTTTTAAGAAAAATCTTTGAGTTTGTTTCTA
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTTTTAAGAAAAACCTTTGAGATTGTTTCTA
*
512848 -TGAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTAA-AATCAACCTTTGAGATTGTTTC
1 TTG-AAACAAA-TTTTGTCTCTCTTGAGACAGTTTTT-TTAAGAA-AAACCTTTGAGATTGTTTC
*
512911 CA
62 TA
* * *
512913 TTGAAACATATTTTGTCTCCCTTGAGGCAGTTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTT
512946 CTATGGAAAC
Statistics
Matches: 181, Mismatches: 30, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
60 2 0.01
61 24 0.13
62 10 0.06
63 15 0.08
64 48 0.27
65 40 0.22
66 28 0.15
67 14 0.08
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (63 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTTTTAAGAAAAACCTTTGAGATTGTTTCTA
Found at i:512978 original size:31 final size:32
Alignment explanation
Indices: 512943--513002 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
512933 CTTGAGGCAG
*
512943 TTTCTATGGAAACACAAT-ATCTTTGAGTTTA
1 TTTCTATGGAAACAAAATCATCTTTGAGTTTA
* *
512974 TTTCTCTTGAAACAAAATCATCTTTGAGT
1 TTTCTATGGAAACAAAATCATCTTTGAGT
513003 CGTTTCCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (32 bp):
TTTCTATGGAAACAAAATCATCTTTGAGTTTA
Found at i:513015 original size:30 final size:31
Alignment explanation
Indices: 512951--513016 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
512941 AGTTTCTATG
* *
512951 GAAACACAATATCTTTGAGTTTATTTCTCTT
1 GAAACAAAATATCTTTGAGTTCATTTCTCTT
*
512982 GAAACAAAATCATCTTTGAG-TCGTTTC-CTT
1 GAAACAAAAT-ATCTTTGAGTTCATTTCTCTT
513012 GAAAC
1 GAAAC
513017 GAATTTTGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.26
31 14 0.45
32 9 0.29
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (31 bp):
GAAACAAAATATCTTTGAGTTCATTTCTCTT
Found at i:513294 original size:129 final size:126
Alignment explanation
Indices: 513128--513567 Score: 450
Period size: 129 Copynumber: 3.4 Consensus size: 126
513118 TAGGAACCGT
* * *
513128 GTCATCCCCCGACCAGACCTCCTCATCATGTAGGAGCCATGTCACCCTTGATAACCAATCGTCCT
1 GTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAA-CATCCT
* * * *
513193 CATCGCGTAGGAACCGTGTTATCGCCCTTCCGAAATATGGTCAGAACTCTTCATCACATATGA
65 CATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGG-CAGAACTCTTCATCACATATGA
* * * *
513256 GTCGTGCCCCCGACCAAACCTCCTCATCACGTAGGAGCCATATCACCCCTGATAACTAACAATCC
1 GTCAT-CCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAAC-ATCC
* * * * * * *
513321 TCATCACATAGGAACCATGTTATCACCCTCCCTAAAGATGGCATACCGTCCTCATCGTGTAGGA-
64 TCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAAC-TCTTCATC----A-CAT
*
513385 ACTGT
123 A-TGA
* * **
513390 GTCATCCCCCGATCAGACCTCCTAATCACGTAGGAGCTGTGTCACCCCTGATAACCAAACATCCT
1 GTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACC-AACATCCT
*
513455 CATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACTCTTCATCACGTATGAGCA
65 CATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACTCTTCATCACATAT--G-A
* * * * * *
513520 GTGTCATCCCCCGATCAGATCTCCTTATCACATAGGATCCGTGTCACC
1 --GTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACC
513568 TTTAGATGTC
Statistics
Matches: 255, Mismatches: 41, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
127 1 0.00
128 11 0.04
129 93 0.36
132 48 0.19
133 92 0.36
134 10 0.04
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (126 bp):
GTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAACATCCTC
ATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACTCTTCATCACATATGA
Found at i:513591 original size:133 final size:130
Alignment explanation
Indices: 513110--513567 Score: 510
Period size: 133 Copynumber: 3.5 Consensus size: 130
513100 TATGCTATCC
*
513110 TCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATCATGTAGGAGCCATGTCACCC
1 TCATCACGTAGGAA-CGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
* * * * * *
513175 TTGATAACCAATCGTCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCGAAATATGGTCAGAAC
65 CTGATAACCAA-CATCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGG-CAGAAC
513240 TCT
128 TCT
* * * * *
513243 TCATCACATATG-A-GTCGT--GCCCCCGACCAAACCTCCTCATCACGTAGGAGCCATATCACCC
1 TCATCACGTAGGAACGT-GTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
* * * * * *
513304 CTGATAACTAACAATCCTCATCACATAGGAACCATGTTATCACCCTCCCTAAAGATGGCATACCG
65 CTGATAACCAAC-ATCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAAC-
*
513369 TCC
128 TCT
** * * **
513372 TCATCGTGTAGGAACTGTGTCATCCCCCGATCAGACCTCCTAATCACGTAGGAGCTGTGTCACCC
1 TCATCACGTAGGAAC-GTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCC
513437 CTGATAACCAAACATCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACT
65 CTGATAACC-AACATCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACT
513502 CT
129 CT
* * * * * * * *
513504 TCATCACGTATGAGCAGTGTCATCCCCCGATCAGATCTCCTTATCACATAGGATCCGTGTCACC
1 TCATCACGTAGGAAC-GTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACC
513568 TTTAGATGTC
Statistics
Matches: 269, Mismatches: 47, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
128 5 0.02
129 95 0.35
130 3 0.01
131 4 0.01
132 59 0.22
133 100 0.37
134 3 0.01
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (130 bp):
TCATCACGTAGGAACGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCC
TGATAACCAACATCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACTCT
Found at i:513768 original size:3 final size:3
Alignment explanation
Indices: 513760--513834 Score: 93
Period size: 3 Copynumber: 25.3 Consensus size: 3
513750 CTACTAAAAA
513760 TAT TAT TAT TA- TAT TAT TAT TA- TAT TAAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* *
513804 TAT AAT TTT TAT TAT TAT TAAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
513835 TACACATTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.10
3 51 0.81
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:515275 original size:29 final size:30
Alignment explanation
Indices: 515243--515320 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
515233 TTATTTGTAA
*
515243 TTACTATTTTAGTCCTTTTAG-TTACTA-TT
1 TTACTATTTTAGTCCTTTAAGATT-CTATTT
**
515272 TTACTA-TTTAACCCTTTAAGATTCTATTT
1 TTACTATTTTAGTCCTTTAAGATTCTATTT
515301 TTACTATTTTAGTCCTTTAA
1 TTACTATTTTAGTCCTTTAA
515321 ATATCTGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 14 0.34
29 16 0.39
30 11 0.27
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.55
Consensus pattern (30 bp):
TTACTATTTTAGTCCTTTAAGATTCTATTT
Found at i:519670 original size:51 final size:48
Alignment explanation
Indices: 519644--519758 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 48
519634 AAGAGCAAAG
*
519644 AAGCAAAGGAAAAAACAAAGAACAAAGAGAAACAAAGCAAAAAAAAAAAAA
1 AAGCAAAGAAAAAAACAAAGAAC-AA-AG-AACAAAGCAAAAAAAAAAAAA
* * * *
519695 AAGCAAAGAAAAAAACAAAGAGCAAAGAA-GAA--AAATAAAGAAAAA
1 AAGCAAAGAAAAAAACAAAGAACAAAGAACAAAGCAAAAAAAAAAAAA
* *
519740 AATCAAAGAAAAGAACAAA
1 AAGCAAAGAAAAAAACAAA
519759 ATAAAGAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
45 28 0.49
47 2 0.04
48 2 0.04
49 2 0.04
50 2 0.04
51 21 0.37
ACGTcount: A:0.76, C:0.09, G:0.14, T:0.02
Consensus pattern (48 bp):
AAGCAAAGAAAAAAACAAAGAACAAAGAACAAAGCAAAAAAAAAAAAA
Found at i:519682 original size:34 final size:31
Alignment explanation
Indices: 519644--519751 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 31
519634 AAGAGCAAAG
*
519644 AAGCAAAGGAAAAAACAAAGAA-CAAAGAGAAACA
1 AAGCAAA-GAAAAAA-AAAAAAGCAAAGA-AAA-A
519678 AAGCAAA-AAAAAAAAAAAAGCAAAGAAAAA
1 AAGCAAAGAAAAAAAAAAAAGCAAAGAAAAA
* *
519708 AA-CAAAGAGCAAAGAAGAAAAA-TAAAGAAAAA
1 AAGCAAAGA--AAA-AAAAAAAAGCAAAGAAAAA
*
519740 AATCAAAGAAAA
1 AAGCAAAGAAAA
519752 GAACAAAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
29 4 0.06
30 4 0.06
31 11 0.17
32 26 0.40
33 13 0.20
34 7 0.11
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.02
Consensus pattern (31 bp):
AAGCAAAGAAAAAAAAAAAAGCAAAGAAAAA
Found at i:519713 original size:44 final size:45
Alignment explanation
Indices: 519664--519758 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 45
519654 AAAAACAAAG
519664 AACAAAGAG-AAACAAAGCAAAAA-AAA-AAAAAAAGCAAAGAAAAA
1 AACAAAGAGCAAA-AAAG-AAAAATAAAGAAAAAAAGCAAAGAAAAA
* * *
519708 AACAAAGAGCAAAGAAGAAAAATAAAGAAAAAAATCAAAGAAAAG
1 AACAAAGAGCAAAAAAGAAAAATAAAGAAAAAAAGCAAAGAAAAA
519753 AACAAA
1 AACAAA
519759 ATAAAGAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 5 0.11
44 15 0.33
45 25 0.56
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.02
Consensus pattern (45 bp):
AACAAAGAGCAAAAAAGAAAAATAAAGAAAAAAAGCAAAGAAAAA
Found at i:519742 original size:12 final size:13
Alignment explanation
Indices: 519717--519751 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
519707 AAACAAAGAG
519717 CAAAGAAGAAAAAT
1 CAAAGAA-AAAAAT
519731 -AAAGAAAAAAAT
1 CAAAGAAAAAAAT
519743 CAAAGAAAA
1 CAAAGAAAA
519752 GAACAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.77, C:0.06, G:0.11, T:0.06
Consensus pattern (13 bp):
CAAAGAAAAAAAT
Found at i:519753 original size:50 final size:50
Alignment explanation
Indices: 519648--519766 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
519638 GCAAAGAAGC
* *
519648 AAAGGAAAAAACAAAGAACAAAGAGAAACAAAGCAAAAAAAAAAAAAAAGC
1 AAAGAAAAAAACAAAGAACAAAGAGAAACAAA-CAAAAAAAAAAAAAAAGA
* * **
519699 AAAGAAAAAAACAAAGAGCAAAGAAGAAA-AATA-AAGAAAAAAATCAAAGA
1 AAAGAAAAAAACAAAGAACAAAG-AGAAACAA-ACAAAAAAAAAAAAAAAGA
* *
519749 AAAGAACAAAATAAAGAA
1 AAAGAAAAAAACAAAGAA
519767 AGAATACAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
50 28 0.49
51 23 0.40
52 6 0.11
ACGTcount: A:0.76, C:0.08, G:0.13, T:0.03
Consensus pattern (50 bp):
AAAGAAAAAAACAAAGAACAAAGAGAAACAAACAAAAAAAAAAAAAAAGA
Found at i:519754 original size:18 final size:17
Alignment explanation
Indices: 519677--519767 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
519667 AAAGAGAAAC
*
519677 AAAGCAAAA-AAAAAAAA
1 AAAG-AAAAGAAAAAAAT
* *
519694 AAAGCAAAGAAAAAAAC
1 AAAGAAAAGAAAAAAAT
519711 AAAGAGCAAAGAAGAAAAAT
1 AAAGA--AAAGAA-AAAAAT
519731 -----AAAGAAAAAAAT
1 AAAGAAAAGAAAAAAAT
*
519743 CAAAGAAAAGAACAAAAT
1 -AAAGAAAAGAAAAAAAT
519761 AAAGAAA
1 AAAGAAA
519768 GAATACAAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
12 6 0.10
13 6 0.10
16 3 0.05
17 22 0.37
18 11 0.19
19 6 0.10
20 5 0.08
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGAAAAAAAT
Found at i:519766 original size:17 final size:18
Alignment explanation
Indices: 519731--519767 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
519721 GAAGAAAAAT
519731 AAAGAAAAAAATCAAAGA
1 AAAGAAAAAAATCAAAGA
*
519749 AAAGAACAAAAT-AAAGA
1 AAAGAAAAAAATCAAAGA
519766 AA
1 AA
519768 GAATACAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAAATCAAAGA
Found at i:521379 original size:17 final size:18
Alignment explanation
Indices: 521340--521381 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
521330 TAGGTATCAG
*
521340 AGCTTGACTCATTAGAAA
1 AGCTTAACTCATTAGAAA
*
521358 A-CTTAACTCGTTA-AAA
1 AGCTTAACTCATTAGAAA
521374 AGCTTAAC
1 AGCTTAAC
521382 ATCCTTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 16 0.76
18 1 0.05
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (18 bp):
AGCTTAACTCATTAGAAA
Found at i:522127 original size:15 final size:15
Alignment explanation
Indices: 522090--522127 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
522080 GATATTGAAA
522090 GAAGAAGAAAAAAAT
1 GAAGAAGAAAAAAAT
522105 GAAG-AGAATAAAAAT
1 GAAGAAGAA-AAAAAT
522120 -AAGAAGAA
1 GAAGAAGAA
522128 GAAAGAGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (15 bp):
GAAGAAGAAAAAAAT
Found at i:529459 original size:65 final size:64
Alignment explanation
Indices: 529340--529477 Score: 147
Period size: 65 Copynumber: 2.1 Consensus size: 64
529330 AAACAAATTG
* * * *
529340 TCTCTTGAGATAGTTTTTTTTAAGAAAAATCTTTGAGTCTGTTTCTATGAAAACAAAGTTTTATC
1 TCTCTTGAGACAGTTTTTCTTAAGAAAAACCTTTGAGTCTGTTTCCATGAAAACAAA-TTTTATC
* * *
529405 TCTCTTGAGACAGTTTTTCTTAA-AATCAACCTTTGAGAT-TGTTTCCATTG-AAACATATTTTG
1 TCTCTTGAGACAGTTTTTCTTAAGAA-AAACCTTTGAG-TCTGTTTCCA-TGAAAACAAATTTTA
529467 TC
63 TC
*
529469 TCCCTTGAG
1 TCTCTTGAG
529478 GCAGATTCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
64 16 0.26
65 43 0.69
66 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (64 bp):
TCTCTTGAGACAGTTTTTCTTAAGAAAAACCTTTGAGTCTGTTTCCATGAAAACAAATTTTATC
Found at i:529554 original size:30 final size:31
Alignment explanation
Indices: 529483--529555 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
529473 TTGAGGCAGA
* * *
529483 TTCTATTGAAACACAATATCTTTGAGTTTAT
1 TTCTCTTGAAACAAAATATCTTTGAGTTCAT
*
529514 TTCTCTTGAAACAAAATCATCTTTGAG-TCGT
1 TTCTCTTGAAACAAAAT-ATCTTTGAGTTCAT
529545 TTC-CTTGAAAC
1 TTCTCTTGAAAC
529556 GAATTTTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 8 0.22
31 20 0.54
32 9 0.24
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (31 bp):
TTCTCTTGAAACAAAATATCTTTGAGTTCAT
Found at i:529566 original size:97 final size:99
Alignment explanation
Indices: 529426--529627 Score: 236
Period size: 97 Copynumber: 2.1 Consensus size: 99
529416 AGTTTTTCTT
* *
529426 AAAATCAACCTTTGAGATTGTTTCCATTGAAACATATTTTGTCTCCCTTGAGGCAGATTCTATTG
1 AAAATCAACCTTTGAGATCGTTTCCATTGAAACATATTTTGTCTCCCTTGAGACAGATTCTATTG
* **
529491 AAACA-CAATATCTTTGAGTTTATTTCTCTTGAAA-C
66 AAACATC---ATCTTTAAGTAGATTTCTCTTGAAACC
* * * *
529526 AAAATC-ATCTTTGAG-TCGTTTCC-TTGAAACGA-ATTTTGTCTCTCTTGAGACAGCTTCTCTT
1 AAAATCAACCTTTGAGATCGTTTCCATTGAAAC-ATATTTTGTCTCCCTTGAGACAGATTCTATT
*
529587 GAAGCATCATCTTTAAGTAGATTTCTCTTGAAACC
65 GAAACATCATCTTTAAGTAGATTTCTCTTGAAACC
529622 AAAATC
1 AAAATC
529628 CCTAAAGATG
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
95 22 0.25
96 7 0.08
97 37 0.42
98 9 0.10
99 8 0.09
100 6 0.07
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (99 bp):
AAAATCAACCTTTGAGATCGTTTCCATTGAAACATATTTTGTCTCCCTTGAGACAGATTCTATTG
AAACATCATCTTTAAGTAGATTTCTCTTGAAACC
Found at i:529963 original size:40 final size:40
Alignment explanation
Indices: 529908--530012 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 40
529898 TGGCATGCCG
**
529908 TCCTCATCGTGTAGGAACTGTGTCATCCCCCG-ACCAGACC-
1 TCCTCATCACGTAGGAACTGTGTCA-CCCCCGAACCAG-CCA
* *
529948 TCCTCATCACGTAGGAGCTGTGTCACCCCTGATAACCAGCCA
1 TCCTCATCACGTAGGAACTGTGTCACCCCCG--AACCAGCCA
*
529990 TCCTCATCACGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACTGTGT
530013 TATTACCCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.09
40 22 0.40
41 2 0.04
42 26 0.47
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACTGTGTCACCCCCGAACCAGCCA
Found at i:530096 original size:133 final size:131
Alignment explanation
Indices: 529664--530089 Score: 511
Period size: 133 Copynumber: 3.2 Consensus size: 131
529654 ACGTAGGAAC
* * * *
529664 CGTGTCATCCCCCTACCAGACCTCCTCATCACGTAAGAGCCATGTCACCCTTGATAACCAACCGT
1 CGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAACCAT
* * * * *
529729 CCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAATATGGTCAGAACTCTTCATCATATATG
66 CCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGG-CAGAACTCTTCATCGTGTATG
529794 AG
130 AG
* * *
529796 TCGTG---T-CCCCGACCAAACCTCCTCATCACGTAGGATCCATGTCACCCCTGATAACCAACAA
1 -CGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAACCA
* * * * *
529857 TCCTCATCACATAGGAACCATGTTATCACCCTCCCTAAAGATGGCATG-CCGTCCTCATCGTGTA
65 TCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCA-GAAC-TCTTCATCGTGTA
* *
529921 GGAA
128 TGAG
** *
529925 CTGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTGATAACCAGCCA
1 C-GTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAACCA
* *
529990 TCCTCATCACGTAGGAACCGTGTTATTACCCTTCCTAAAGATGGCCAGAACTCTTCATCGCGTAT
65 TCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGG-CAGAACTCTTCATCGTGTAT
530055 GAG
129 GAG
* * *
530058 CAGTGTCATCCCCCGATCAGATCTCCTAATCA
1 C-GTGTCATCCCCCGACCAGACCTCCTCATCA
530090 TATAGGATTC
Statistics
Matches: 246, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
128 4 0.02
129 102 0.41
130 1 0.00
132 1 0.00
133 135 0.55
134 3 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.24
Consensus pattern (131 bp):
CGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTGATAACCAACCAT
CCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAGAACTCTTCATCGTGTATGA
G
Found at i:530308 original size:3 final size:3
Alignment explanation
Indices: 530300--530356 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
530290 CTACTAAAAA
530300 TAT TAT TAT T-T TAT TAT TAT TA- TAT TAAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
530344 TAAT TAT T-T TAT T
1 T-AT TAT TAT TAT T
530357 TACACATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:530336 original size:21 final size:19
Alignment explanation
Indices: 530300--530356 Score: 86
Period size: 18 Copynumber: 3.2 Consensus size: 19
530290 CTACTAAAAA
530300 TATTATTATT--TTATTAT
1 TATTATTATTAATTATTAT
530317 TATTA-TATTAATTATTAT
1 TATTATTATTAATTATTAT
530335 TATTATTATTAATTATT-T
1 TATTATTATTAATTATTAT
530353 TATT
1 TATT
530357 TACACATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.11
17 5 0.14
18 17 0.46
19 11 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTATTAATTATTAT
Found at i:531795 original size:29 final size:30
Alignment explanation
Indices: 531763--531840 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
531753 TTATTTGTAA
*
531763 TTACTATTTTAGTCCTTTTAG-TTGATA-TT
1 TTACTATTTTAGTCCTTTAAGATT-ATATTT
** *
531792 TTACTA-TTTAACCCTTTAAGATTCTATTT
1 TTACTATTTTAGTCCTTTAAGATTATATTT
531821 TTACTATTTTAGTCCTTTAA
1 TTACTATTTTAGTCCTTTAA
531841 ATATCTGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 13 0.32
29 16 0.40
30 11 0.28
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.55
Consensus pattern (30 bp):
TTACTATTTTAGTCCTTTAAGATTATATTT
Found at i:543071 original size:29 final size:29
Alignment explanation
Indices: 543033--543112 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
543023 ATGTGATATA
543033 AGAACATGACATGAGCTACATGATCACAAG
1 AGAA-ATGACATGAGCTACATGATCACAAG
*
543063 AGAAATGACATGAGCTACATGATCATAAG
1 AGAAATGACATGAGCTACATGATCACAAG
*
543092 ATAAATGACATGAG-TACATGA
1 AGAAATGACATGAGCTACATGA
543113 ACATATGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.15
29 37 0.77
30 4 0.08
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (29 bp):
AGAAATGACATGAGCTACATGATCACAAG
Found at i:543215 original size:15 final size:15
Alignment explanation
Indices: 543197--543230 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
543187 GAGGGTATAC
543197 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
543212 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
543227 TAGT
1 TAGT
543231 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:548986 original size:29 final size:29
Alignment explanation
Indices: 548947--549027 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
548937 TATATGATAT
548947 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
* *
548977 GAGAAATGACATAAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
549006 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
549028 ACATATGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 7 0.15
29 36 0.75
30 5 0.10
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:549014 original size:15 final size:15
Alignment explanation
Indices: 548967--549014 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
548957 CATGAGCTAC
*
548967 ATGATCACAAGAGAA
1 ATGATCATAAGAGAA
** *
548982 ATGA-CATAAGCTAC
1 ATGATCATAAGAGAA
548996 ATGATCATAAGAGAA
1 ATGATCATAAGAGAA
549011 ATGA
1 ATGA
549015 CATGAGTACA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (15 bp):
ATGATCATAAGAGAA
Found at i:549130 original size:15 final size:15
Alignment explanation
Indices: 549112--549145 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
549102 GAGGGTATAA
549112 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
549127 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
549142 TAGT
1 TAGT
549146 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:553683 original size:20 final size:20
Alignment explanation
Indices: 553625--553683 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
553615 GCCACTTTTT
553625 CTTTATTTCTTTGCACTTTATCA
1 CTTTATTTC-TTG-A-TTTATCA
* *
553648 CTTT-GTTCTATAATTTATCA
1 CTTTATTTCT-TGATTTATCA
553668 CTTTATTTCTTGATTT
1 CTTTATTTCTTGATTT
553684 TTTTCGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 16 0.53
21 6 0.20
22 4 0.13
23 4 0.13
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.59
Consensus pattern (20 bp):
CTTTATTTCTTGATTTATCA
Found at i:554522 original size:60 final size:58
Alignment explanation
Indices: 554440--554558 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 58
554430 AATAATGATC
554440 TTCATTTAAATTAGTCCTCAAAC-TTTTAAATATTTCAATTTCATCTTCAAACTATGACA
1 TTCATTTAAATTAGTCCTCAAACTTTTTAAATATTTCAATTTCATC-TCAAACTAT-ACA
*
554499 TTCATTCTAAATTAGTGCC-CAAACTTTTTGAATATTTCAATTTCATCTCAAACTATACA
1 TTCATT-TAAATTAGT-CCTCAAACTTTTTAAATATTTCAATTTCATCTCAAACTATACA
554558 T
1 T
554559 ATATACTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
59 10 0.18
60 23 0.41
61 23 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (58 bp):
TTCATTTAAATTAGTCCTCAAACTTTTTAAATATTTCAATTTCATCTCAAACTATACA
Done.