Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 194 of 199
Found at i:56328463 original size:44 final size:43
Alignment explanation
Indices: 56328364--56328471 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 43
56328354 AGCTAAGTCT
* * **
56328364 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATC
1 TATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATC
*
56328407 TCATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGCGACAAATC
1 T-ATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATC
*
56328451 T-TGTACCTTTGAAGTTACAGT
1 TATCT-CC-TTGAAGTTACAGT
56328472 AGGTCGGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
42 2 0.04
43 3 0.05
44 50 0.91
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (43 bp):
TATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATC
Found at i:56329858 original size:16 final size:17
Alignment explanation
Indices: 56329837--56329869 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56329827 ATGTCTAGGT
56329837 AAATT-ATTAATTGAGA
1 AAATTAATTAATTGAGA
56329853 AAATTAGATTAATTGAG
1 AAATTA-ATTAATTGAG
56329870 GGGTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
AAATTAATTAATTGAGA
Found at i:56331360 original size:46 final size:46
Alignment explanation
Indices: 56331293--56331433 Score: 246
Period size: 46 Copynumber: 3.1 Consensus size: 46
56331283 TATGGCAAAG
* * *
56331293 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
56331339 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
*
56331385 TGTGAAAAGTAGGTATGGTATTCCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
56331431 TGT
1 TGT
56331434 AGCAATGTGA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
Found at i:56332706 original size:3 final size:3
Alignment explanation
Indices: 56332689--56332783 Score: 59
Period size: 3 Copynumber: 32.0 Consensus size: 3
56332679 CGTTATTTTC
* * ** *
56332689 ATT ATT AGT AGT ATT ATT ATT -TAT ATT ATT AAA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
56332734 ATT AAT GTC ATC ATT ACT A-T AGT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56332781 ATT
1 ATT
56332784 CACTTATTTA
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
2 3 0.04
3 69 0.95
4 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:56332882 original size:18 final size:18
Alignment explanation
Indices: 56332847--56332882 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56332837 ACTTGTATTT
*
56332847 TTTTTATAATATACATAC
1 TTTTTATAATACACATAC
*
56332865 TTTTTATAATACATATAC
1 TTTTTATAATACACATAC
56332883 ACGTACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTATAATACACATAC
Found at i:56333193 original size:24 final size:21
Alignment explanation
Indices: 56333166--56333208 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 21
56333156 ATATTTTAAT
56333166 TTACATACGTATATATGTATATGC
1 TTACATA--TATATAT-TATATGC
56333190 TTACATATATATATTATAT
1 TTACATATATATATTATAT
56333209 AATAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
24 7 0.37
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (21 bp):
TTACATATATATATTATATGC
Found at i:56340447 original size:19 final size:19
Alignment explanation
Indices: 56340420--56340458 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
56340410 TCAATCATCT
*
56340420 ACAGGAAATATACAC-GCAA
1 ACAGCAAATA-ACACAGCAA
56340439 ACAGCAAATAACACAGCAA
1 ACAGCAAATAACACAGCAA
56340458 A
1 A
56340459 AATAGCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (19 bp):
ACAGCAAATAACACAGCAA
Found at i:56341527 original size:16 final size:16
Alignment explanation
Indices: 56341508--56341543 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
56341498 TTATTTAGTT
56341508 ATTTATTTA-TTCTTGC
1 ATTTATTTATTTCTT-C
56341524 ATTTATTTATTTCTTC
1 ATTTATTTATTTCTTC
56341540 ATTT
1 ATTT
56341544 CCCTTGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTATTTATTTCTTC
Found at i:56353304 original size:24 final size:24
Alignment explanation
Indices: 56353256--56353310 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
56353246 TATTCAATTT
56353256 TCATA-TTTCAATTCAATCACTTTC
1 TCATATTTTCAATTCAATCAC-TTC
*
56353280 TCATATTTTCCATTCAAATCA-TTC
1 TCATATTTTCAATTC-AATCACTTC
56353304 TCA-ATTT
1 TCATATTT
56353311 AATCACAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 11 0.39
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (24 bp):
TCATATTTTCAATTCAATCACTTC
Found at i:56375448 original size:37 final size:37
Alignment explanation
Indices: 56375406--56375479 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
56375396 TCCTCACAAC
*
56375406 ATTTTTGCTCTTACTCTTTCTTCTAACAAGTTCCATG
1 ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTCCATG
*
56375443 ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTTCATG
1 ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTCCATG
56375480 GTATACTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (37 bp):
ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTCCATG
Found at i:56379104 original size:22 final size:22
Alignment explanation
Indices: 56379055--56379104 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
56379045 GGTTCAATTG
56379055 AATAAATTATTAAAAATAAAAT
1 AATAAATTATTAAAAATAAAAT
*
56379077 ATTAAA-TATTAAAAAATAGAAA-
1 AATAAATTATT-AAAAATA-AAAT
56379099 AATAAA
1 AATAAA
56379105 AAAATTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.17
22 17 0.71
23 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAAATTATTAAAAATAAAAT
Found at i:56380578 original size:20 final size:20
Alignment explanation
Indices: 56380553--56380594 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
56380543 CTATTTCATA
*
56380553 TTTAGTAAATTATATTAAAT
1 TTTAGTAAATTACATTAAAT
**
56380573 TTTAGTGTATTACATTAAAT
1 TTTAGTAAATTACATTAAAT
56380593 TT
1 TT
56380595 CAAACTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTAGTAAATTACATTAAAT
Found at i:56384297 original size:18 final size:18
Alignment explanation
Indices: 56384276--56384338 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
56384266 ATTTTTCCTA
56384276 TAAAAAATATTAAAAAAT
1 TAAAAAATATTAAAAAAT
*
56384294 TAAAAAAAATTATCAAAAAT
1 TAAAAAATATTA--AAAAAT
* * *
56384314 ATAAATATTATT-AAATAT
1 -TAAAAAATATTAAAAAAT
56384332 TAAAAAA
1 TAAAAAA
56384339 ATAAAATTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
17 5 0.14
18 16 0.46
20 6 0.17
21 8 0.23
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAATATTAAAAAAT
Found at i:56386014 original size:2 final size:2
Alignment explanation
Indices: 56386009--56386045 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56385999 CACCAATTGA
56386009 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
56386046 TATATACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:56401582 original size:3 final size:3
Alignment explanation
Indices: 56401574--56401636 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
56401564 TATTTTAGTG
* * *
56401574 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56401622 TTA TTAA TTA TTA TT
1 TTA TT-A TTA TTA TT
56401637 GGCTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:56419871 original size:3 final size:3
Alignment explanation
Indices: 56419863--56419900 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
56419853 TAATTCTGTT
56419863 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
56419901 GAGATCAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:56424328 original size:6 final size:6
Alignment explanation
Indices: 56424317--56424341 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56424307 TGAAACAAAA
56424317 TTCACT TTCACT TTCACT TTCACT T
1 TTCACT TTCACT TTCACT TTCACT T
56424342 AGCCGTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCACT
Found at i:56427770 original size:3 final size:3
Alignment explanation
Indices: 56427762--56427790 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56427752 TAATTATTTA
56427762 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56427791 AAGCAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56435205 original size:18 final size:18
Alignment explanation
Indices: 56435178--56435222 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
56435168 AATATTAAAA
56435178 TTTTATTTTAA-AAATAT
1 TTTTATTTTAATAAATAT
*
56435195 TTTTCATTTTAATAATTA-
1 TTTT-ATTTTAATAAATAT
56435213 TTTTATTTTA
1 TTTTATTTTA
56435223 CTATTTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 11 0.44
19 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTTTAATAAATAT
Found at i:56436216 original size:6 final size:6
Alignment explanation
Indices: 56436207--56436276 Score: 122
Period size: 6 Copynumber: 11.5 Consensus size: 6
56436197 AATTTCTCTA
*
56436207 TCTCTC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCCC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCT-CCC
56436256 TCTCCC TCTCCC TCTCCC TCT
1 TCTCCC TCTCCC TCTCCC TCT
56436277 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
6 56 0.90
7 6 0.10
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
TCTCCC
Found at i:56436385 original size:3 final size:3
Alignment explanation
Indices: 56436377--56436459 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
56436367 NNNNNNNNNN
56436377 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
56436425 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
56436460 TCTCTCTCTC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:56436464 original size:2 final size:2
Alignment explanation
Indices: 56436457--56436522 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
56436447 CCTCCTCCTC
56436457 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
56436499 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
56436523 AAATATATTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:56437686 original size:2 final size:2
Alignment explanation
Indices: 56437681--56437737 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
56437671 CACGTTTCTT
56437681 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
56437723 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
56437738 TGTATTGATT
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:56437852 original size:31 final size:33
Alignment explanation
Indices: 56437798--56437858 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
56437788 AAAGTATTTT
*
56437798 TTTTATAAAATTCTAAAATATATA-ATTATAAG
1 TTTTATAAAATTCTAAAAAATATATATTATAAG
56437830 TTTTA-AAAATTC-AAAACAATATATATTAT
1 TTTTATAAAATTCTAAAA-AATATATATTAT
56437859 GTCTGACGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 12 0.46
32 10 0.38
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (33 bp):
TTTTATAAAATTCTAAAAAATATATATTATAAG
Found at i:56437947 original size:50 final size:50
Alignment explanation
Indices: 56437870--56438069 Score: 213
Period size: 50 Copynumber: 4.0 Consensus size: 50
56437860 TCTGACGAGA
56437870 CGAGACGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCAC
1 CGAGACGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCAC
* * * * * *
56437920 CAAGACGAGAGGTCCCATGTGAGACCATGTCTGGGATATGGCGTTGGTAC
1 CGAGACGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCAC
* * ** * * *
56437970 CGAGATGAGAAGTCCCCCGTAAGACCATGTCTGGGACATAGCATGGGCAC
1 CGAGACGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCAC
* * ** *
56438020 CGACATGAGAACATCCCATGTAAGACCATGTCT-AGGACATGGCTTTGGCA
1 CGAGACGAG-AGGTCCCATGTAAGACCATGTCTGA-GACATGGCATTGGCA
56438070 TGTTATTATC
Statistics
Matches: 122, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
50 91 0.75
51 31 0.25
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
CGAGACGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCATTGGCAC
Found at i:56440659 original size:283 final size:280
Alignment explanation
Indices: 56440049--56440894 Score: 1453
Period size: 283 Copynumber: 3.0 Consensus size: 280
56440039 TAATACAAAG
* *
56440049 TTCCATTGAAATAATTACACAAAATCATCAAACATTTCCAATTTGGATTGAAATACTTGACAACT
1 TTCCATTG-AATAAATACACAAAATCATCAAACAATTCCAATTTGGATTGAAATACTTGACAACT
* *
56440114 TAATTAACTTCGACGAGTAAAAGCTTGCGATGAATGACAACTTCCAACAAGTTTACATTTTCATT
65 TAATTAATTTCGACGAGTAAAAGCTTGCGATGAATGACAACTTCCAACAAGTTTCCATTTTCATT
*
56440179 CATCAGCTCAAACACACAAACATCACCCACCTCGAATTCATGTACATCGCAAATTGTCCCCAACT
130 CATCAGCTCAAACACACAAACATCTCCCACCTCGAATTCATGT-CATCGCAAATTGTCCCCAACT
*
56440244 CTTACCCCCAAACACTGCTTTTCTACCTTTACTCCTTCCTCTTCTTTCATACTCATCTTTCCAAC
194 CTTACCCCCAAACACTGCTTTTCTACCTTTACTCCTTCCTCTTCTTTCATACTCAACTTTCCAAC
*
56440309 TCCTCCCATCCGCAACTCTCAG
259 TCCTCCCATCCGCAACTCTCAA
*
56440331 TTCCATTGAATAAATACACAAAATCATCAAACAATTCCAATTTGGATTGAAATACTTGATAACTT
1 TTCCATTGAATAAATACACAAAATCATCAAACAATTCCAATTTGGATTGAAATACTTGACAACTT
56440396 AATTAATTTCGACGAGTAAAAGCTTGCGAT-AAGTGACAACTTCCAACAAGTTTCCATTTTCATT
66 AATTAATTTCGACGAGTAAAAGCTTGCGATGAA-TGACAACTTCCAACAAGTTTCCATTTTCATT
*
56440460 CATCAGCTCAAACACACAAACATCTCCCACCTCGAATTCATGGTCTATTGCAAATTGTCCCCCAA
130 CATCAGCTCAAACACACAAACATCTCCCACCTCGAATTCAT-GTC-ATCGCAAATTGT-CCCCAA
* *
56440525 TTCTTACCCCCAACCACTGCTTTTCTACCTTTACTCCTTCCTCTTCTTTCATACTCAACTTTCCA
192 CTCTTACCCCCAAACACTGCTTTTCTACCTTTACTCCTTCCTCTTCTTTCATACTCAACTTTCCA
56440590 ACTCCTCCCATCCGCAACTCTCAA
257 ACTCCTCCCATCCGCAACTCTCAA
*
56440614 TTCCATTGAATAAATACACAAAATCATCAAACAGTTCCAATTTGGATTGAAATACTTGACAACTT
1 TTCCATTGAATAAATACACAAAATCATCAAACAATTCCAATTTGGATTGAAATACTTGACAACTT
*
56440679 AATTAATTTCGATGAGTAAAAGCTTGCGATGAATGACAACTTCCAACAAGTTTCCATTTTCATTC
66 AATTAATTTCGACGAGTAAAAGCTTGCGATGAATGACAACTTCCAACAAGTTTCCATTTTCATTC
*
56440744 ATCAGCTCAAACACACAAACGTCTCCCACCTCGAATTCATTGTCCATCGCAAATTGTCCCCAACT
131 ATCAGCTCAAACACACAAACATCTCCCACCTCGAATTCA-TGT-CATCGCAAATTGTCCCCAACT
* *
56440809 CTTACCCTCAAACACTGCTTTTCTA-CTTGTACTCCTTCCTCTTCTTTCATACTCAACATTCCAA
194 CTTACCCCCAAACACTGCTTTTCTACCTT-TACTCCTTCCTCTTCTTTCATACTCAACTTTCCAA
56440873 CTCCTCCCATCCGCAACTCTCA
258 CTCCTCCCATCCGCAACTCTCA
56440895 GCATCATTTC
Statistics
Matches: 536, Mismatches: 20, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
280 2 0.00
281 157 0.29
282 107 0.20
283 266 0.50
284 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.31
Consensus pattern (280 bp):
TTCCATTGAATAAATACACAAAATCATCAAACAATTCCAATTTGGATTGAAATACTTGACAACTT
AATTAATTTCGACGAGTAAAAGCTTGCGATGAATGACAACTTCCAACAAGTTTCCATTTTCATTC
ATCAGCTCAAACACACAAACATCTCCCACCTCGAATTCATGTCATCGCAAATTGTCCCCAACTCT
TACCCCCAAACACTGCTTTTCTACCTTTACTCCTTCCTCTTCTTTCATACTCAACTTTCCAACTC
CTCCCATCCGCAACTCTCAA
Found at i:56447361 original size:3 final size:3
Alignment explanation
Indices: 56447353--56447378 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56447343 AGCCTATTCT
56447353 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
56447379 GGTCATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:56452250 original size:16 final size:16
Alignment explanation
Indices: 56452229--56452277 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
56452219 CAAGATTGCT
56452229 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
56452245 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
56452261 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
56452277 A
1 A
56452278 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:56465229 original size:21 final size:22
Alignment explanation
Indices: 56465174--56465229 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 22
56465164 ACTAAGACTC
56465174 AATCGACAATTCTGAAGCGCATT
1 AATCGACAATT-TGAAGCGCATT
** *
56465197 -ATCCTCCTATTT-AAGCGCATT
1 AAT-CGACAATTTGAAGCGCATT
56465218 AATCGACAATTT
1 AATCGACAATTT
56465230 TTTCATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
21 15 0.60
22 5 0.20
23 5 0.20
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (22 bp):
AATCGACAATTTGAAGCGCATT
Found at i:56471010 original size:6 final size:6
Alignment explanation
Indices: 56470999--56471023 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56470989 TTCTTAAAAT
56470999 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
56471024 CCGGCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:56474947 original size:20 final size:21
Alignment explanation
Indices: 56474919--56474962 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
56474909 TTTATATGAT
56474919 AATTAAAAAAAATA-AAATCA
1 AATTAAAAAAAATAGAAATCA
* *
56474939 AATTGAAAAAAATAGAAATGA
1 AATTAAAAAAAATAGAAATCA
56474960 AAT
1 AAT
56474963 GTTACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (21 bp):
AATTAAAAAAAATAGAAATCA
Found at i:56479841 original size:7 final size:7
Alignment explanation
Indices: 56479814--56479853 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
56479804 CTACTATAAT
56479814 ATTAAAA
1 ATTAAAA
56479821 A-TAAAA
1 ATTAAAA
* *
56479827 ACTCAAA
1 ATTAAAA
56479834 ATTAAAA
1 ATTAAAA
56479841 ATTAAAA
1 ATTAAAA
56479848 ATTAAA
1 ATTAAA
56479854 GTGCAAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (7 bp):
ATTAAAA
Found at i:56484098 original size:28 final size:27
Alignment explanation
Indices: 56484066--56484136 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
56484056 TTTTGGGATT
*
56484066 AAATTTTAGGGTTTAACATAATTTTTAA
1 AAATTTTAGGGTTTAACAGAA-TTTTAA
* **
56484094 AAATTTTACGAGTTTAATGGAATTTTAA
1 AAATTTTA-GGGTTTAACAGAATTTTAA
*
56484122 AAA-TTAAGGGTTTAA
1 AAATTTTAGGGTTTAA
56484137 TTAAAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.19
27 3 0.08
28 17 0.47
29 9 0.25
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (27 bp):
AAATTTTAGGGTTTAACAGAATTTTAA
Found at i:56484117 original size:29 final size:28
Alignment explanation
Indices: 56484088--56484186 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
56484078 TTAACATAAT
*
56484088 TTTTAAAAATTTTACGAGTTTAATGGAA
1 TTTTAAAAATTTTAAGAGTTTAATGGAA
* **
56484116 TTTTAAAAA--TTAAGGGTTTAATTAAAA
1 TTTTAAAAATTTTAAGAGTTTAA-TGGAA
* ** * *
56484143 TTTTTAATTTTTTATGAGATTAATGAGAA
1 TTTTAAAAATTTTAAGAGTTTAATG-GAA
56484172 TTTTAAAAATTTTAA
1 TTTTAAAAATTTTAA
56484187 AAGAGATCAA
Statistics
Matches: 51, Mismatches: 16, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
26 10 0.20
27 9 0.18
28 10 0.20
29 22 0.43
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.46
Consensus pattern (28 bp):
TTTTAAAAATTTTAAGAGTTTAATGGAA
Found at i:56484300 original size:20 final size:20
Alignment explanation
Indices: 56484263--56484302 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
56484253 AATTAAAGAA
* **
56484263 TTTTTAAAATTTTTAATTTT
1 TTTTTAAAACTTCAAATTTT
56484283 TTTTTAAAACTTCAAATTTT
1 TTTTTAAAACTTCAAATTTT
56484303 CCAAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAAAACTTCAAATTTT
Found at i:56486629 original size:14 final size:14
Alignment explanation
Indices: 56486610--56486644 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56486600 TACAATATCC
56486610 AAATAGTAACAACA
1 AAATAGTAACAACA
*
56486624 AAATAGTAACATCA
1 AAATAGTAACAACA
*
56486638 TAATAGT
1 AAATAGT
56486645 GAAATAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:56488825 original size:18 final size:18
Alignment explanation
Indices: 56488798--56488836 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
56488788 AAATTTGAAA
*
56488798 TAACATAATAGAAAACAC
1 TAACACAATAGAAAACAC
56488816 TAACACAATAGAAAACAC
1 TAACACAATAGAAAACAC
56488834 TAA
1 TAA
56488837 AGAATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.18, G:0.05, T:0.15
Consensus pattern (18 bp):
TAACACAATAGAAAACAC
Found at i:56488920 original size:14 final size:14
Alignment explanation
Indices: 56488901--56488928 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56488891 ATCATTAGAT
56488901 AAATCAAAATTTAA
1 AAATCAAAATTTAA
56488915 AAATCAAAATTTAA
1 AAATCAAAATTTAA
56488929 GCTAAAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATCAAAATTTAA
Found at i:56489769 original size:2 final size:2
Alignment explanation
Indices: 56489762--56489800 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56489752 TTAATTTCAG
56489762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56489801 GATGTTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56492606 original size:2 final size:2
Alignment explanation
Indices: 56492601--56492634 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56492591 TCTCTTTTGC
56492601 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
56492635 CAGTAGGTAA
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):
TA
Found at i:56497477 original size:13 final size:13
Alignment explanation
Indices: 56497459--56497483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56497449 ACGAAATTCA
56497459 AATTAAAAAATTT
1 AATTAAAAAATTT
56497472 AATTAAAAAATT
1 AATTAAAAAATT
56497484 CTCAAATTCC
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAAAAATTT
Found at i:56518111 original size:20 final size:21
Alignment explanation
Indices: 56518064--56518111 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
56518054 AATTTTTAAA
56518064 TAATTTAATGACTTAAATAAT
1 TAATTTAATGACTTAAATAAT
** * *
56518085 TTTTTTAAT-AGTTAAATGAT
1 TAATTTAATGACTTAAATAAT
56518105 TAATTTA
1 TAATTTA
56518112 TAACTTTTTG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (21 bp):
TAATTTAATGACTTAAATAAT
Found at i:56534671 original size:2 final size:2
Alignment explanation
Indices: 56534666--56534708 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
56534656 ATAAAAAATA
56534666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56534707 AT
1 AT
56534709 GGTAATGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56535246 original size:32 final size:31
Alignment explanation
Indices: 56535181--56535247 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
56535171 CGTAAAAACA
* *
56535181 CAATAACTTAAATAAAAACTTTTGAATAATT
1 CAATAACTTAAATAAAAAATTTTAAATAATT
* *
56535212 CAATAATTTAAATAAAAAATTTTCAAATAGTT
1 CAATAACTTAAATAAAAAATTTT-AAATAATT
56535244 CAAT
1 CAAT
56535248 GACTGTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (31 bp):
CAATAACTTAAATAAAAAATTTTAAATAATT
Found at i:56535444 original size:3 final size:3
Alignment explanation
Indices: 56535436--56535468 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
56535426 GTATATTTTA
56535436 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56535469 ATTTAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56535748 original size:2 final size:2
Alignment explanation
Indices: 56535741--56535788 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
56535731 TCTAGTCGTG
56535741 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
56535783 AT AT AT
1 AT AT AT
56535789 GGGATTTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56536386 original size:13 final size:14
Alignment explanation
Indices: 56536360--56536388 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56536350 AAAATGTTTG
56536360 TTTGTATATATTAT
1 TTTGTATATATTAT
56536374 TTTGTAT-TATTAT
1 TTTGTATATATTAT
56536387 TT
1 TT
56536389 ATCATATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
TTTGTATATATTAT
Found at i:56543736 original size:20 final size:20
Alignment explanation
Indices: 56543711--56543755 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
56543701 AATAATTCGA
*
56543711 AAATTTTTATTTAAGTCACT
1 AAATTTTTATTTAAATCACT
*
56543731 AAATTTTTATTTAAATTACT
1 AAATTTTTATTTAAATCACT
56543751 AAATT
1 AAATT
56543756 CTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTTTTATTTAAATCACT
Found at i:56547500 original size:13 final size:13
Alignment explanation
Indices: 56547482--56547507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56547472 TTTAAGAAGC
56547482 GGACAAATCGATT
1 GGACAAATCGATT
56547495 GGACAAATCGATT
1 GGACAAATCGATT
56547508 TGATTCTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GGACAAATCGATT
Found at i:56548174 original size:60 final size:61
Alignment explanation
Indices: 56548039--56548184 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 61
56548029 GGACCTAAAT
* * * * *
56548039 TTTTTTTTGATCCAAGTTTAAGCCCTGAATTTGGTAATTCTTCTCACATTTGGGGCATGAAC
1 TTTTTTTTGATCCAAG-TTAGGCCTTAAACTTGGCAATTCTTCTCACATTTGGGGCATGAAC
* * * *
56548101 TTTTTTGT-ATCCAAGTTAGGCCTTAAACTTGGCAATTCTTTTTACA-TTGGGGCTTGAAC
1 TTTTTTTTGATCCAAGTTAGGCCTTAAACTTGGCAATTCTTCTCACATTTGGGGCATGAAC
* * *
56548160 TTTTTTTTGGTCCAAATTAGTCCTT
1 TTTTTTTTGATCCAAGTTAGGCCTT
56548185 GAAAACCTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 19 0.27
60 37 0.53
61 7 0.10
62 7 0.10
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (61 bp):
TTTTTTTTGATCCAAGTTAGGCCTTAAACTTGGCAATTCTTCTCACATTTGGGGCATGAAC
Found at i:56548837 original size:30 final size:29
Alignment explanation
Indices: 56548803--56548874 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
56548793 GTCTTTGTAC
*
56548803 CTTTTATAGATTTGGAATTTAGTCTCTATA
1 CTTTTATAGATTT-GAATTTAGTCCCTATA
** *
56548833 CTTTTATTTATATGAATTTAGTCCCTATA
1 CTTTTATAGATTTGAATTTAGTCCCTATA
56548862 CATTTT-TAGATTT
1 C-TTTTATAGATTT
56548875 CAAAATTTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (29 bp):
CTTTTATAGATTTGAATTTAGTCCCTATA
Found at i:56549780 original size:18 final size:18
Alignment explanation
Indices: 56549753--56549792 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
56549743 ACATTACGTG
56549753 AAAAACTAAATAAAATAA
1 AAAAACTAAATAAAATAA
* *
56549771 AAAAATTAAATTAAATAA
1 AAAAACTAAATAAAATAA
56549789 AAAA
1 AAAA
56549793 GGAAGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAACTAAATAAAATAA
Found at i:56562933 original size:4 final size:4
Alignment explanation
Indices: 56562924--56562954 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
56562914 TTGCGTGCAC
*
56562924 CATA CATA CATA CATA CATA CAAA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
56562955 GTAAAGAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:56567787 original size:13 final size:13
Alignment explanation
Indices: 56567769--56567793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56567759 TTTTATTTGT
56567769 TTATTCCCACCGA
1 TTATTCCCACCGA
56567782 TTATTCCCACCG
1 TTATTCCCACCG
56567794 GTCGAATGTT
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:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:56569780 original size:12 final size:12
Alignment explanation
Indices: 56569763--56569796 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
56569753 GTTATTTATT
56569763 TTCTTTTGCTCG
1 TTCTTTTGCTCG
*
56569775 TTCTTTGGCTCG
1 TTCTTTTGCTCG
56569787 TTCTTTTGCT
1 TTCTTTTGCT
56569797 TAAAATGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.18, T:0.59
Consensus pattern (12 bp):
TTCTTTTGCTCG
Found at i:56570837 original size:49 final size:49
Alignment explanation
Indices: 56570780--56570883 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
56570770 TCATGTGTTA
* * ** * *
56570780 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
56570829 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
56570878 TAATTT
1 TAATTT
56570884 ATTTTTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:56572366 original size:13 final size:13
Alignment explanation
Indices: 56572358--56572409 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
56572348 ATTATTATTA
*
56572358 AATTATATTTAAT
1 AATTATATTTTAT
56572371 AATTATTATTTTA-
1 AATTA-TATTTTAT
56572384 AATTATATTTTAGT
1 AATTATATTTTA-T
*
56572398 -ATTATATATTAT
1 AATTATATTTTAT
56572410 GATTTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
12 8 0.24
13 20 0.59
14 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
AATTATATTTTAT
Found at i:56572402 original size:26 final size:27
Alignment explanation
Indices: 56572242--56572393 Score: 95
Period size: 25 Copynumber: 5.7 Consensus size: 27
56572232 TAATAAAGTA
*
56572242 TATTA-TAAATTATATTTAATAATAAT
1 TATTATTAAATTATATTTAATAATTAT
* *
56572268 TA-T-TTAAATTATATTTTAT-AGTAT
1 TATTATTAAATTATATTTAATAATTAT
* *
56572292 TATATATT--ATGAT-TTTAGTAAATTCAT
1 TAT-TATTAAATTATATTTAAT-AATT-AT
** * * *
56572319 ATAAGAATAAGAATTTTATTTAATTATTTAT
1 -T-ATTATTA-AATTATATTTAA-TAATTAT
56572350 TATTATTAAATTATATTTAATAATTAT
1 TATTATTAAATTATATTTAATAATTAT
56572377 TATT-TTAAATTATATTT
1 TATTATTAAATTATATTT
56572394 TAGTATTATA
Statistics
Matches: 93, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
24 9 0.10
25 19 0.20
26 18 0.19
27 14 0.15
28 14 0.15
29 5 0.05
30 1 0.01
31 5 0.05
32 7 0.08
33 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (27 bp):
TATTATTAAATTATATTTAATAATTAT
Found at i:56572487 original size:15 final size:17
Alignment explanation
Indices: 56572449--56572482 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56572439 TTTATTAACA
56572449 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
56572466 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
56572483 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:56572496 original size:16 final size:15
Alignment explanation
Indices: 56572449--56572496 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
56572439 TTTATTAACA
*
56572449 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
56572466 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
56572481 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
56572497 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:56572674 original size:39 final size:39
Alignment explanation
Indices: 56572626--56572734 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 39
56572616 TTTTTTCCTT
* * *
56572626 ATACTATTACACCTCTATTCCATTCAACCAAACACAAGA
1 ATACCATTACGCCTCTATTCCATTCAACCAAACAAAAGA
56572665 ATACCATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGA
1 ATACCATTACGCCTCTATT-C----CATTCAACCAAACAAAAGA
56572709 ATTACCTATTACGCCTCTATTCCATT
1 A-TACC-ATTACGCCTCTATTCCATT
56572735 ACGCCTCTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
39 17 0.28
40 1 0.02
41 4 0.07
44 19 0.32
45 5 0.08
46 14 0.23
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (39 bp):
ATACCATTACGCCTCTATTCCATTCAACCAAACAAAAGA
Found at i:56572709 original size:44 final size:46
Alignment explanation
Indices: 56572646--56572736 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
56572636 ACCTCTATTC
*
56572646 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
56572690 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
56572736 C
1 C
56572737 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:56572737 original size:16 final size:16
Alignment explanation
Indices: 56572716--56572752 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
56572706 AGAATTACCT
56572716 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
56572732 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
56572748 ATTAC
1 ATTAC
56572753 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:56572825 original size:22 final size:23
Alignment explanation
Indices: 56572800--56572843 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
56572790 TACATTTTTT
*
56572800 ATTTAGTTGTATTT-TTAATTTG
1 ATTTAGTTGAATTTATTAATTTG
*
56572822 ATTTATTTGAATTTATTAATTT
1 ATTTAGTTGAATTTATTAATTT
56572844 TAGTTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (23 bp):
ATTTAGTTGAATTTATTAATTTG
Found at i:56576937 original size:14 final size:14
Alignment explanation
Indices: 56576914--56576944 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56576904 TATTGCGTTC
*
56576914 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
56576928 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
56576942 TTA
1 TTA
56576945 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:56578300 original size:11 final size:11
Alignment explanation
Indices: 56578274--56578306 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
56578264 TTTCATTTTT
56578274 TAAAAATAAAA
1 TAAAAATAAAA
56578285 T-AAAATAAAA
1 TAAAAATAAAA
*
56578295 TAAAAATTAAA
1 TAAAAATAAAA
56578306 T
1 T
56578307 TGTGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:56589283 original size:22 final size:23
Alignment explanation
Indices: 56589245--56589287 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
56589235 TCGTAAAATT
56589245 AAAAATGAAAAACGAATCAATCC
1 AAAAATGAAAAACGAATCAATCC
56589268 AAAAAT-AATAAA-GAATCAAT
1 AAAAATGAA-AAACGAATCAAT
56589288 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (23 bp):
AAAAATGAAAAACGAATCAATCC
Found at i:56590557 original size:19 final size:19
Alignment explanation
Indices: 56590535--56590571 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56590525 CTTGCCCATT
*
56590535 GCAAGAGAAGTAGAGAAAA
1 GCAAGAGAAGCAGAGAAAA
56590554 GCAAGAGAAGCAGAGAAA
1 GCAAGAGAAGCAGAGAAA
56590572 GAAAAACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.08, G:0.32, T:0.03
Consensus pattern (19 bp):
GCAAGAGAAGCAGAGAAAA
Found at i:56590612 original size:38 final size:38
Alignment explanation
Indices: 56590556--56590631 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
56590546 AGAGAAAAGC
*
56590556 AAGAGAAGCAGAGAAAGAAAAACAGGGATTGATGAAGA
1 AAGAGAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
*
56590594 AAGATAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
1 AAGAGAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
56590632 TGAGAGAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.57, C:0.05, G:0.29, T:0.09
Consensus pattern (38 bp):
AAGAGAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
Found at i:56590972 original size:38 final size:38
Alignment explanation
Indices: 56590919--56590991 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
56590909 TACCCATTGC
* *
56590919 AAGAGAAGCAGAGAAAGAAAAATAGGGATTGATGAAGA
1 AAGAGAAGCAGAGAAAGAAAAACAGGGATCGATGAAGA
*
56590957 AAGAGAAGCATAGAAAGAAAAACAGGGATCGATGA
1 AAGAGAAGCAGAGAAAGAAAAACAGGGATCGATGA
56590992 CGAGAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.55, C:0.05, G:0.30, T:0.10
Consensus pattern (38 bp):
AAGAGAAGCAGAGAAAGAAAAACAGGGATCGATGAAGA
Found at i:56594360 original size:2 final size:2
Alignment explanation
Indices: 56594353--56594379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56594343 AGAACAGAGT
56594353 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
56594380 TACCTTGAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56594922 original size:15 final size:16
Alignment explanation
Indices: 56594890--56594921 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56594880 AATCCAAATT
*
56594890 ATTTAAATTAAAAAAA
1 ATTTAAACTAAAAAAA
56594906 ATTTAAACTAAAAAAA
1 ATTTAAACTAAAAAAA
56594922 TCAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTTAAACTAAAAAAA
Found at i:56605121 original size:24 final size:25
Alignment explanation
Indices: 56605082--56605137 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
56605072 CATAGATCAG
* *
56605082 TTTTTAATAGTAAAAATGGATGAAA
1 TTTTTAACAGTAAAAATGAATGAAA
56605107 TTTTTAACAGTAAAAATGAATGAAA
1 TTTTTAACAGTAAAAATGAATGAAA
56605132 TTTTTA
1 TTTTTA
56605138 GGAGAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (25 bp):
TTTTTAACAGTAAAAATGAATGAAA
Found at i:56611701 original size:27 final size:27
Alignment explanation
Indices: 56611671--56611722 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
56611661 TGACTAAAAC
56611671 AGAAAAA-TTCAAATAGTTGGGTGACAA
1 AGAAAAAGTT-AAATAGTTGGGTGACAA
*
56611698 AGAAAAAGTTTAATAGTTGGGTGAC
1 AGAAAAAGTTAAATAGTTGGGTGAC
56611723 TATTTTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (27 bp):
AGAAAAAGTTAAATAGTTGGGTGACAA
Found at i:56618558 original size:2 final size:2
Alignment explanation
Indices: 56618551--56618575 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56618541 TTACAAAAAC
56618551 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
56618576 TTGATTGTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56619932 original size:96 final size:96
Alignment explanation
Indices: 56619768--56619965 Score: 369
Period size: 96 Copynumber: 2.1 Consensus size: 96
56619758 CAATTCAACC
* *
56619768 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTTCGGTAGCTGATTT
1 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
56619833 AATAGGTTCCAAGTCCCCAACATAATTTATT
66 AATAGGTTCCAAGTCCCCAACATAATTTATT
*
56619864 GATTTCAATACTAAAGAAGGGGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
1 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
56619929 AATAGGTTCCAAGTCCCCAACATAATTTATT
66 AATAGGTTCCAAGTCCCCAACATAATTTATT
56619960 GATTTC
1 GATTTC
56619966 TAAAGTGGCT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (96 bp):
GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
AATAGGTTCCAAGTCCCCAACATAATTTATT
Found at i:56620357 original size:25 final size:24
Alignment explanation
Indices: 56620323--56620374 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56620313 GTTTTAATTT
* *
56620323 AAAAAAAAACCTGGTAAAAAAATA
1 AAAAAAAAAACTGATAAAAAAATA
* *
56620347 AAAAAAAAAACTGATAGAAGAATA
1 AAAAAAAAAACTGATAAAAAAATA
56620371 AAAA
1 AAAA
56620375 GAAGGGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.12
Consensus pattern (24 bp):
AAAAAAAAAACTGATAAAAAAATA
Found at i:56625764 original size:5 final size:5
Alignment explanation
Indices: 56625754--56625778 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56625744 TTACTATCAG
56625754 CTGTA CTGTA CTGTA CTGTA CTGTA
1 CTGTA CTGTA CTGTA CTGTA CTGTA
56625779 ATGGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
CTGTA
Found at i:56627827 original size:16 final size:16
Alignment explanation
Indices: 56627806--56627856 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
56627796 GATAATTATT
56627806 TTACATATAATATAAA
1 TTACATATAATATAAA
56627822 TTACATAATATATATAAA
1 TTACAT-ATA-ATATAAA
*
56627840 GTAACATAT--TATAAA
1 -TTACATATAATATAAA
56627855 TT
1 TT
56627857 TGAAGACGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.03
15 6 0.20
16 6 0.20
17 3 0.10
18 9 0.30
19 5 0.17
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (16 bp):
TTACATATAATATAAA
Found at i:56627846 original size:19 final size:18
Alignment explanation
Indices: 56627810--56627852 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
56627800 ATTATTTTAC
*
56627810 ATATAATATAAATTACATA
1 ATAT-ATATAAATAACATA
56627829 ATATATATAAAGTAACATA
1 ATATATATAAA-TAACATA
*
56627848 TTATA
1 ATATA
56627853 AATTTGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (18 bp):
ATATATATAAATAACATA
Found at i:56629066 original size:29 final size:29
Alignment explanation
Indices: 56629004--56629066 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
56628994 TTGCTACTCG
*
56629004 ACTATGAAAAGTTAAAAAATAGTCATCCA
1 ACTATAAAAAGTTAAAAAATAGTCATCCA
* * * *
56629033 GCTATAAAAAGTTACAAAATGGTCATCGA
1 ACTATAAAAAGTTAAAAAATAGTCATCCA
56629062 ACTAT
1 ACTAT
56629067 TCAATTTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (29 bp):
ACTATAAAAAGTTAAAAAATAGTCATCCA
Found at i:56630771 original size:11 final size:11
Alignment explanation
Indices: 56630755--56630784 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
56630745 TTTTATTATT
56630755 TATTTTTAAAA
1 TATTTTTAAAA
56630766 TATTTTTAAAA
1 TATTTTTAAAA
56630777 TACTTTTT
1 TA-TTTTT
56630785 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:56631075 original size:6 final size:6
Alignment explanation
Indices: 56631064--56631090 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56631054 TTTGTCATTG
56631064 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
56631091 CACTCAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:56636356 original size:16 final size:16
Alignment explanation
Indices: 56636335--56636365 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56636325 TGAATGGCTA
*
56636335 AAAATTTAAAAAATAC
1 AAAATTCAAAAAATAC
56636351 AAAATTCAAAAAATA
1 AAAATTCAAAAAATA
56636366 ATTTATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATTCAAAAAATAC
Found at i:56643171 original size:22 final size:22
Alignment explanation
Indices: 56643128--56643172 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
56643118 AAGTCTGAGT
* *
56643128 AAGACTCAAACTTGAATACTTA
1 AAGACTCAAACCTCAATACTTA
56643150 AAGACTCAATACCTCAAT-CTTA
1 AAGACTCAA-ACCTCAATACTTA
56643172 A
1 A
56643173 CCAATAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (22 bp):
AAGACTCAAACCTCAATACTTA
Found at i:56667694 original size:20 final size:20
Alignment explanation
Indices: 56667663--56667713 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
56667653 TTTTATCACA
* *
56667663 CACACAAAAAAAAATTAAAAT
1 CACATAAAAAACAA-TAAAAT
56667684 CACATAAAAAATCAATAAAAT
1 CACATAAAAAA-CAATAAAAT
56667705 -ACATAAAAA
1 CACATAAAAA
56667714 TAAGCATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
21 16 0.59
22 2 0.07
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.16
Consensus pattern (20 bp):
CACATAAAAAACAATAAAAT
Found at i:56670980 original size:4 final size:4
Alignment explanation
Indices: 56670971--56671026 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
56670961 GTGTTGATAG
56670971 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
56671019 ATGT ATGT
1 ATGT ATGT
56671027 GTCGTTTCTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:56671574 original size:98 final size:98
Alignment explanation
Indices: 56671405--56671601 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
56671395 TTAACAGTAT
** * * *
56671405 TAACAATTGGACTTGAAGTTTGAAATCTAAAAAGTAGAGGAACTAAATTCCTGGAAATAAAAGTA
1 TAACAATTAAACTTGAAGTTTGAAACCTAAAAAGCAGAGGAACTAAATTCCTGGAAATAAAAATA
* *
56671470 CATTTTCAAATTTGTGAAGAGTATAGGGATCTA
66 CATTTTCAAATTTGTGAAGAGAATAGGGACCTA
56671503 TAACAATTAAACTTGAAGTTTGAAACCTAAAAAGCAGAGGAACTAAATTCCTGGAAATAAAAATA
1 TAACAATTAAACTTGAAGTTTGAAACCTAAAAAGCAGAGGAACTAAATTCCTGGAAATAAAAATA
56671568 CATTTTCAAATTTGTGAAGAGAATAGGGACCTA
66 CATTTTCAAATTTGTGAAGAGAATAGGGACCTA
56671601 T
1 T
56671602 GACATATTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (98 bp):
TAACAATTAAACTTGAAGTTTGAAACCTAAAAAGCAGAGGAACTAAATTCCTGGAAATAAAAATA
CATTTTCAAATTTGTGAAGAGAATAGGGACCTA
Found at i:56671659 original size:31 final size:31
Alignment explanation
Indices: 56671622--56671699 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
56671612 AATCTATACT
* *
56671622 AATTGGTACTTCAA-TTTAGCTTCAATGTTCT
1 AATTGGTACTT-AAGTTTAGCTTCAATATTCA
* * * *
56671653 ACTTGGTGCCTAAGTTTGGCTTCAATATTCA
1 AATTGGTACTTAAGTTTAGCTTCAATATTCA
56671684 AATTGGTACTTAAGTT
1 AATTGGTACTTAAGTT
56671700 ATTTTCCATT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (31 bp):
AATTGGTACTTAAGTTTAGCTTCAATATTCA
Found at i:56672065 original size:6 final size:6
Alignment explanation
Indices: 56672033--56672063 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
56672023 AACCACAACC
*
56672033 ACAAAT ACAAAT ACAAAT ACAAAT ATAAAT A
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT A
56672064 TATATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (6 bp):
ACAAAT
Found at i:56677967 original size:2 final size:2
Alignment explanation
Indices: 56677960--56677985 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56677950 ATTATGCTAA
56677960 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
56677986 TTTACATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56680337 original size:12 final size:11
Alignment explanation
Indices: 56680320--56680349 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
56680310 ACAAAGGTGC
56680320 TTTATTTATTT
1 TTTATTTATTT
56680331 GTTTATTTATTT
1 -TTTATTTATTT
56680343 TTTATTT
1 TTTATTT
56680350 TGAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:56681198 original size:3 final size:3
Alignment explanation
Indices: 56681174--56681334 Score: 91
Period size: 3 Copynumber: 54.3 Consensus size: 3
56681164 ATATCTTTGC
* * * *
56681174 TAT T-T TAT CAT TAT TTT TAT TAT TAG TAG TAT TAT TAT T-T ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* ** * * * *
56681218 TAT TAT TAT TAT TAT TAA CGT CAT CAT TAC TA- TAG TAT TAT TAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * *
56681265 TAT TACT T-T TAT TAC TAT TAT TTT TGT TAT TAT TAA TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
56681310 TAG TAT TACT T-T TAT TAT TAA TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT T
56681335 GTCACTACTA
Statistics
Matches: 123, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
2 10 0.08
3 107 0.87
4 6 0.05
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:56684591 original size:2 final size:2
Alignment explanation
Indices: 56684586--56684640 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
56684576 NNAATCTCTC
56684586 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
56684628 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
56684641 TATGAGACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56685075 original size:2 final size:2
Alignment explanation
Indices: 56685068--56685107 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
56685058 AGGTTGACAA
* *
56685068 AT AT AT AT AT AT AT AC AT AT AT AT AC 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
56685108 GCATAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:56688296 original size:2 final size:2
Alignment explanation
Indices: 56688291--56688316 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56688281 AGTGTGTGTG
56688291 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
56688317 ACAAGTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56690777 original size:12 final size:12
Alignment explanation
Indices: 56690760--56690784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56690750 TTTTAATCAG
56690760 AATAAAGTATTT
1 AATAAAGTATTT
56690772 AATAAAGTATTT
1 AATAAAGTATTT
56690784 A
1 A
56690785 GACTAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATAAAGTATTT
Found at i:56696313 original size:23 final size:21
Alignment explanation
Indices: 56696267--56696316 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
56696257 GCCAACGCCT
*
56696267 GCAAAAAAGACAGAAAAGAGA
1 GCAAAAAAGACAGAAAACAGA
56696288 GCAAAAATAG-CAGAGAAACAGTA
1 GCAAAAA-AGACAGA-AAACAG-A
56696311 GCAAAA
1 GCAAAA
56696317 GTAAATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 7 0.28
23 7 0.28
ACGTcount: A:0.62, C:0.12, G:0.22, T:0.04
Consensus pattern (21 bp):
GCAAAAAAGACAGAAAACAGA
Found at i:56698993 original size:18 final size:18
Alignment explanation
Indices: 56698972--56699006 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56698962 TTCGGTTTTG
*
56698972 TAAAATTACATTAAAATA
1 TAAAAATACATTAAAATA
56698990 TAAAAATACATTAAAAT
1 TAAAAATACATTAAAAT
56699007 CACATTACAT
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:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATACATTAAAATA
Found at i:56702600 original size:30 final size:30
Alignment explanation
Indices: 56702564--56702634 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
56702554 TTAGCTGTAC
*
56702564 TTGCATTGTTGTTTGAGACAGTTTTTCTAT
1 TTGCATTGTTGTTTGAGACAATTTTTCTAT
* *
56702594 TTGCATTGTTATTTGAGACAATTTTTGTAT
1 TTGCATTGTTGTTTGAGACAATTTTTCTAT
56702624 TTGCATTGTTG
1 TTGCATTGTTG
56702635 ACAATTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.54
Consensus pattern (30 bp):
TTGCATTGTTGTTTGAGACAATTTTTCTAT
Found at i:56709408 original size:41 final size:42
Alignment explanation
Indices: 56709363--56709455 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
56709353 TTCTAATTAT
* * * *
56709363 AAGCGTTTTTAACGGATTTG-C-AAGAAAACGTTTCCAGCTGA
1 AAGCGTTTTCAACGGA-TTGACAAAAAAAACGATTCCAACTGA
* *
56709404 AAGCGTTTTCAATGGATTGACAAAAAAAATGATTCCAACTGA
1 AAGCGTTTTCAACGGATTGACAAAAAAAACGATTCCAACTGA
56709446 AAGCGTTTTC
1 AAGCGTTTTC
56709456 TACCTCCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.07
41 15 0.34
42 26 0.59
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (42 bp):
AAGCGTTTTCAACGGATTGACAAAAAAAACGATTCCAACTGA
Found at i:56713565 original size:21 final size:22
Alignment explanation
Indices: 56713539--56713584 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
56713529 AAAATCTAAA
* *
56713539 AAAAGTAAAA-ATTTAAATTTT
1 AAAAGTAAAAGAATCAAATTTT
56713560 AAAAGTAAAAGAATCAAATTTT
1 AAAAGTAAAAGAATCAAATTTT
56713582 AAA
1 AAA
56713585 TTTACGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
AAAAGTAAAAGAATCAAATTTT
Found at i:56718328 original size:43 final size:42
Alignment explanation
Indices: 56718233--56718463 Score: 200
Period size: 43 Copynumber: 5.4 Consensus size: 42
56718223 ATGCAATATC
* * * *
56718233 CCAGATATGGTCTTACATGTAATCTCGTATCGATGCCAATAG-
1 CCAGACATGGTCTTACACGAAATCTCATATCGATGCCAAT-GT
* * * *
56718275 CTCAGCCATGGTCTTACACGAAATCACGTATCGATACCAATGT
1 C-CAGACATGGTCTTACACGAAATCTCATATCGATGCCAATGT
* * * *
56718318 CCAAGACATGGTCTTACAAG-AATCCTTATATCAATGCCATAT-C
1 CC-AGACATGGTCTTACACGAAAT-CTCATATCGATGCCA-ATGT
* * * *
56718361 CCAAATATGGTCTTACACAAAATCGCATATCGATGCCAATGT
1 CCAGACATGGTCTTACACGAAATCTCATATCGATGCCAATGT
* *
56718403 CGCAGACATGGTCTTACACGAATTCTCATATCGATGCCATAT-C
1 C-CAGACATGGTCTTACACGAAATCTCATATCGATGCCA-ATGT
*
56718446 CCAGATATGGTCTTACAC
1 CCAGACATGGTCTTACAC
56718464 AGTAGCACAT
Statistics
Matches: 151, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.01
42 48 0.32
43 97 0.64
44 4 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
CCAGACATGGTCTTACACGAAATCTCATATCGATGCCAATGT
Found at i:56718384 original size:85 final size:85
Alignment explanation
Indices: 56718282--56718464 Score: 269
Period size: 85 Copynumber: 2.2 Consensus size: 85
56718272 TAGCTCAGCC
* * *
56718282 ATGGTCTTACACGAAATCACGTATCGATACCAATGTC-CAAGACATGGTCTTACAAGAATCCTTA
1 ATGGTCTTACACAAAATCACATATCGATACCAATGTCGC-AGACATGGTCTTACAAGAATCCTCA
56718346 TATCAATGCCATATCCCAAAT
65 TATCAATGCCATATCCCAAAT
* * * *
56718367 ATGGTCTTACACAAAATCGCATATCGATGCCAATGTCGCAGACATGGTCTTACACGAATTCTCAT
1 ATGGTCTTACACAAAATCACATATCGATACCAATGTCGCAGACATGGTCTTACAAGAATCCTCAT
* *
56718432 ATCGATGCCATATCCCAGAT
66 ATCAATGCCATATCCCAAAT
56718452 ATGGTCTTACACA
1 ATGGTCTTACACA
56718465 GTAGCACATA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 87 0.99
86 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (85 bp):
ATGGTCTTACACAAAATCACATATCGATACCAATGTCGCAGACATGGTCTTACAAGAATCCTCAT
ATCAATGCCATATCCCAAAT
Found at i:56718475 original size:85 final size:84
Alignment explanation
Indices: 56718233--56718476 Score: 267
Period size: 85 Copynumber: 2.9 Consensus size: 84
56718223 ATGCAATATC
* * * * * **
56718233 CCAGATATGGTCTTACATGTAA-TCTCGTATCGATGCCAATAGCTCAGCCATGGTCTTACAC-GA
1 CCAGACATGGTCTTACAAG-AATTCTCATATCGATGCC-ATATCCCAGATATGGTCTTACACAG-
*
56718296 AATCACGTATCGATACCAATGT
63 AATCACATATCGATACCAATGT
* * * * *
56718318 CCAAGACATGGTCTTACAAGAATCCTTATATCAATGCCATATCCCAAATATGGTCTTACACAAAA
1 CC-AGACATGGTCTTACAAGAATTCTCATATCGATGCCATATCCCAGATATGGTCTTACACAGAA
* *
56718383 TCGCATATCGATGCCAATGT
65 TCACATATCGATACCAATGT
* *
56718403 CGCAGACATGGTCTTACACGAATTCTCATATCGATGCCATATCCCAGATATGGTCTTACACAGTA
1 C-CAGACATGGTCTTACAAGAATTCTCATATCGATGCCATATCCCAGATATGGTCTTACACAGAA
*
56718468 GCACATATC
65 TCACATATC
56718477 ACACCGATGC
Statistics
Matches: 131, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
85 104 0.79
86 27 0.21
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (84 bp):
CCAGACATGGTCTTACAAGAATTCTCATATCGATGCCATATCCCAGATATGGTCTTACACAGAAT
CACATATCGATACCAATGT
Found at i:56718532 original size:53 final size:53
Alignment explanation
Indices: 56718474--56718581 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
56718464 AGTAGCACAT
* * * *
56718474 ATCACACCGATGCCATATCCTAGATATGGTCTTATACAGAAA-CTCATAATCAC
1 ATCACACCAATGCCATAGCCCAGATATGGTCTTATACAGAAATCACAT-ATCAC
* *
56718527 ATCACACCAATGCCATAGCCCAGCTATGGTCTTATACGGAAATCACATATCAC
1 ATCACACCAATGCCATAGCCCAGATATGGTCTTATACAGAAATCACATATCAC
56718580 AT
1 AT
56718582 GTTGCCATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
53 44 0.92
54 4 0.08
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (53 bp):
ATCACACCAATGCCATAGCCCAGATATGGTCTTATACAGAAATCACATATCAC
Found at i:56721159 original size:6 final size:6
Alignment explanation
Indices: 56721150--56721180 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
56721140 ATATTTATTG
*
56721150 GTTTTT GTTTTT GTTTTT GTATTT GTTTTT G
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT G
56721181 ATTCCCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.19, T:0.77
Consensus pattern (6 bp):
GTTTTT
Found at i:56721165 original size:12 final size:12
Alignment explanation
Indices: 56721145--56721180 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
56721135 TACTTATATT
*
56721145 TATTGGTTTTTG
1 TATTTGTTTTTG
*
56721157 TTTTTGTTTTTG
1 TATTTGTTTTTG
56721169 TATTTGTTTTTG
1 TATTTGTTTTTG
56721181 ATTCCCAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.00, G:0.19, T:0.75
Consensus pattern (12 bp):
TATTTGTTTTTG
Found at i:56722895 original size:17 final size:17
Alignment explanation
Indices: 56722862--56722893 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56722852 TTCTAAATAT
56722862 TATTTTTTAATAATTTA
1 TATTTTTTAATAATTTA
56722879 TATTTTTT-ATAATTT
1 TATTTTTTAATAATTT
56722894 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTTAATAATTTA
Found at i:56723107 original size:17 final size:18
Alignment explanation
Indices: 56723057--56723107 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
56723047 TAATTTTTAC
*
56723057 ATATTTCTATA-ATTTTT
1 ATATATCTATACATTTTT
56723074 ATATAT-TATACCA-TTTT
1 ATATATCTATA-CATTTTT
56723091 ATA-ATCTATACATTTTT
1 ATATATCTATACATTTTT
56723108 TTAAATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 8 0.28
17 20 0.69
18 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATCTATACATTTTT
Found at i:56724921 original size:31 final size:31
Alignment explanation
Indices: 56724851--56724917 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
56724841 TAATTTGACC
*
56724851 AAATTTAG-TCTCTGTACTTTTTGAATTGGTT
1 AAATTTAGTTCTCTGTACTTTTCGAATT-GTT
56724882 AAATTTAGTTCT-TGTACTTTTCGAATT-TT
1 AAATTTAGTTCTCTGTACTTTTCGAATTGTT
56724911 GAAATTT
1 -AAATTT
56724918 TAGTCGTAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 2 0.06
30 6 0.18
31 22 0.67
32 3 0.09
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.52
Consensus pattern (31 bp):
AAATTTAGTTCTCTGTACTTTTCGAATTGTT
Found at i:56733066 original size:9 final size:9
Alignment explanation
Indices: 56733052--56733092 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
56733042 CATCCATATA
56733052 ATTTTCAAT
1 ATTTTCAAT
56733061 ATTTTCAAT
1 ATTTTCAAT
*
56733070 ATTTTTAAT
1 ATTTTCAAT
56733079 ATTTTCAAT
1 ATTTTCAAT
56733088 ATTTT
1 ATTTT
56733093 TAAAGTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTTTCAAT
Found at i:56735604 original size:4 final size:4
Alignment explanation
Indices: 56735595--56735634 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
56735585 TTTCATGTAC
* * *
56735595 CATA CATA CATG CATG CATG CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
56735635 TAAATGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:56736137 original size:41 final size:41
Alignment explanation
Indices: 56736080--56736161 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
56736070 AATGAAAAAT
* *
56736080 AAGAATAAAAATTATTAGTATGATAACAAAGTGAAGAAAGG
1 AAGAAGAAAAATTATTAGTATGAGAACAAAGTGAAGAAAGG
56736121 AAGAAGAAAAATTATTAGTATGAGAACAAAGTGAAGAAAGG
1 AAGAAGAAAAATTATTAGTATGAGAACAAAGTGAAGAAAGG
56736162 GTCCAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (41 bp):
AAGAAGAAAAATTATTAGTATGAGAACAAAGTGAAGAAAGG
Found at i:56736871 original size:22 final size:22
Alignment explanation
Indices: 56736840--56736882 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56736830 AACTTCAATG
56736840 TTTTAATTTTAAATATTATTAAA
1 TTTTAATTTTAAATATT-TTAAA
*
56736863 TTTT-ATTTTTAATATTTTAA
1 TTTTAATTTTAAATATTTTAA
56736883 TGAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAATTTTAAATATTTTAAA
Found at i:56738863 original size:8 final size:8
Alignment explanation
Indices: 56738847--56738942 Score: 63
Period size: 9 Copynumber: 11.4 Consensus size: 8
56738837 TTAAGCTATC
56738847 ATATAATA
1 ATATAATA
*
56738855 ATATGATA
1 ATATAATA
*
56738863 AGTAGCAATA
1 A-TA-TAATA
56738873 ATATAAGT-
1 ATATAA-TA
56738881 A-ATAATA
1 ATATAATA
56738888 ATAATAATA
1 AT-ATAATA
56738897 ATAATAATA
1 AT-ATAATA
*
56738906 ACAATAATA
1 A-TATAATA
*
56738915 GTAATAATA
1 AT-ATAATA
56738924 ATAGTAATA
1 ATA-TAATA
56738933 ATA-AATA
1 ATATAATA
56738940 ATA
1 ATA
56738943 AAAGATGATA
Statistics
Matches: 71, Mismatches: 8, Indels: 19
0.72 0.08 0.19
Matches are distributed among these distances:
6 1 0.01
7 12 0.17
8 12 0.17
9 42 0.59
10 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (8 bp):
ATATAATA
Found at i:56738875 original size:3 final size:3
Alignment explanation
Indices: 56738869--56738981 Score: 106
Period size: 3 Copynumber: 36.7 Consensus size: 3
56738859 GATAAGTAGC
*
56738869 AAT AAT -AT AAGT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
56738914 AGT AAT AAT AAT AGT AAT AAT AAAT AAT AAA AGAT GAT AAT ACATT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT AAT A-A-T AAT
56738962 AAT AAT GAAT AA- AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AA
56738982 AAATGCTAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
2 6 0.07
3 71 0.78
4 12 0.13
5 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:56744749 original size:2 final size:2
Alignment explanation
Indices: 56744742--56744794 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
56744732 TGAAGGAATG
56744742 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
56744784 TA TA TA TA TA T
1 TA TA TA TA TA T
56744795 TATTNNNNNN
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56745765 original size:21 final size:20
Alignment explanation
Indices: 56745741--56745780 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
56745731 ATTTTTTTAA
*
56745741 AATTTTCTAATGATTTTTATT
1 AATTTTCTAA-AATTTTTATT
*
56745762 AATTTTTTAAAATTTTTAT
1 AATTTTCTAAAATTTTTAT
56745781 GTAGTACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
AATTTTCTAAAATTTTTATT
Found at i:56746100 original size:17 final size:19
Alignment explanation
Indices: 56746061--56746106 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
56746051 TATTATCGGA
56746061 ATAAAAAATATATATTTCT
1 ATAAAAAATATATATTTCT
*
56746080 -TAAATAAT-TATATTT-T
1 ATAAAAAATATATATTTCT
56746096 AT-AAAAATATA
1 ATAAAAAATATA
56746107 ATTCAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
16 6 0.26
17 10 0.43
18 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAAAATATATATTTCT
Done.