Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_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: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:504494 original size:2 final size:2
Alignment explanation
Indices: 504487--504533 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
504477 TCAATATACA
504487 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
504529 AT AT A
1 AT AT A
504534 CGAAATACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:504708 original size:85 final size:83
Alignment explanation
Indices: 504550--504708 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 83
504540 ACAATCACGT
* * *
504550 CACACGAATGTGTGTCATTTATTTATGACGGGGGCTTCAATGACATGCAATGTAAGTCATATATG
1 CACACAAATGTGTGTCATTTATTTATGACGGGGGCTTCAATGACATGCAATGCAAGTCATAAATG
**
504615 CGTGTCATAAATTTATGA
66 CGCATCATAAATTTATGA
* **
504633 CACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCT-CAATGCGTGTCATAA
1 CACACAAATGTGTGTCAT-TT-ATTTATGACGGGGGCTTCAATGAC-ATGCAATGCAAGTCATAA
504697 ATGCGCATCATA
63 ATGCGCATCATA
504709 GATGTGTGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
83 17 0.26
84 2 0.03
85 45 0.69
86 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (83 bp):
CACACAAATGTGTGTCATTTATTTATGACGGGGGCTTCAATGACATGCAATGCAAGTCATAAATG
CGCATCATAAATTTATGA
Found at i:504717 original size:26 final size:26
Alignment explanation
Indices: 504688--504737 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
504678 CGCTCAATGC
* *
504688 GTGTCATAAATGCGCATCATAGATGT
1 GTGTAATAAATGCACATCATAGATGT
*
504714 GTGTAATAAATGCACGTCATAGAT
1 GTGTAATAAATGCACATCATAGAT
504738 TTATGACACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (26 bp):
GTGTAATAAATGCACATCATAGATGT
Found at i:506256 original size:36 final size:36
Alignment explanation
Indices: 506104--506244 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
506094 TAATTTACTC
*
506104 AAAACAAAGTGTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* * * *
506141 GAAACAAATTGTGTCTCTTTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
506177 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
506213 AAAACAAATTTTGCCTCTCTTGAGATAGTTTC
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTC
506245 CATTGAAACA
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 84 0.92
37 7 0.08
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:506349 original size:21 final size:22
Alignment explanation
Indices: 506305--506358 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
506295 TCTCGAGACA
* * *
506305 GTTTCTTTTGGAACTAAGTTTT
1 GTTTCTCTTGAAACTAAATTTT
506327 GTTTCTCTTGAAAC-AAATTTT
1 GTTTCTCTTGAAACTAAATTTT
*
506348 GTCTCTCTTGA
1 GTTTCTCTTGA
506359 GACAGTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (22 bp):
GTTTCTCTTGAAACTAAATTTT
Found at i:506351 original size:58 final size:58
Alignment explanation
Indices: 506271--506395 Score: 164
Period size: 58 Copynumber: 2.2 Consensus size: 58
506261 TTGAATCTAT
* * * *
506271 TTTC-CTTTAAACAAATTGTGTCTCTCTCGAGACAG-TTTCTTTTGGAACTAAGTTTTG
1 TTTCTCTTGAAACAAATTGTGTCTCTCTCGAGACAGTTTTC-CTTGAAACAAAGTTTTG
* *
506328 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGAAACAAAGTTTTG
1 TTTCTCTTGAAACAAATTGTGTCTCTCTCGAGACAGTTTTCCTTGAAACAAAGTTTTG
*
506386 TCTCTCTTGA
1 TTTCTCTTGA
506396 GATAGTTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 4 0.07
58 51 0.86
59 4 0.07
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.44
Consensus pattern (58 bp):
TTTCTCTTGAAACAAATTGTGTCTCTCTCGAGACAGTTTTCCTTGAAACAAAGTTTTG
Found at i:506373 original size:36 final size:38
Alignment explanation
Indices: 506328--506415 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 38
506318 CTAAGTTTTG
506328 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGT
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
*
506365 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGATAGT
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
*
506402 TTTCTCCTGAAACA
1 TTTCTCTTGAAACA
506416 CCAACCTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 11 0.23
37 28 0.60
38 8 0.17
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (38 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
Found at i:506510 original size:33 final size:33
Alignment explanation
Indices: 506468--506621 Score: 213
Period size: 33 Copynumber: 4.6 Consensus size: 33
506458 CCTGGAGATA
506468 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
506501 GTTTCTCTTGAAACACGAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
506534 G-TTCTCTTGAAACACGAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
506566 GTTTCTCTTGAAACACACACAAAAAACCTTTGAAAAT-
1 GTTTCTCTTG--A-A-ACACAAAAAACCTTTG-AAATC
* *
506603 ATTTCTCTTGGAACACAAA
1 GTTTCTCTTGAAACACAAA
506622 GACCTTCGAG
Statistics
Matches: 111, Mismatches: 4, Indels: 12
0.87 0.03 0.09
Matches are distributed among these distances:
32 32 0.29
33 48 0.43
34 1 0.01
35 1 0.01
36 1 0.01
37 24 0.22
38 4 0.04
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:506766 original size:84 final size:86
Alignment explanation
Indices: 506614--506773 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 86
506604 TTTCTCTTGG
*
506614 AACACAAAGACCTTCGAGTTCAACTACACTCAGCTTCAAAGGCACATCATTTACAACATAGCTCA
1 AACACAAAGACCTTCGAGTTCAACTACACTCAGCTTCAAAGGCACATCATTTACAACATAACTCA
506679 AGGCAAGAAGGGCCATTTGCC
66 AGGCAAGAAGGGCCATTTGCC
* * * * *
506700 AACA-AAAGACCTTCGAGTTCGAGTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTCA
1 AACACAAAGACCTTCGAGTTCAACTACACTCAGCTTCAAAGGCACATCATTTACAACATAACTCA
*
506763 AGGCTAGAAGG
66 AGGCAAGAAGG
506774 TTATATTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 36 0.54
85 27 0.40
86 4 0.06
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (86 bp):
AACACAAAGACCTTCGAGTTCAACTACACTCAGCTTCAAAGGCACATCATTTACAACATAACTCA
AGGCAAGAAGGGCCATTTGCC
Found at i:507454 original size:36 final size:36
Alignment explanation
Indices: 507390--507495 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
507380 CAAACGTTAA
* *
507390 AGTTTTAGTAGGATTTAAACTCCTAAAAATAGGATAG
1 AGTTTTACTAGGA-TTCAACTCCTAAAAATAGGATAG
507427 AGTTTTACTAGGATTCAACTCCTAAAAATAGGATAG
1 AGTTTTACTAGGATTCAACTCCTAAAAATAGGATAG
*
507463 AGTTTTACTATGATTCAAGCTCCTAAAAATAGG
1 AGTTTTACTAGGATTCAA-CTCCTAAAAATAGG
507496 TTCCACAAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 39 0.60
37 26 0.40
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (36 bp):
AGTTTTACTAGGATTCAACTCCTAAAAATAGGATAG
Found at i:508074 original size:9 final size:9
Alignment explanation
Indices: 508062--508226 Score: 65
Period size: 9 Copynumber: 17.8 Consensus size: 9
508052 CATATATATT
508062 TTATTTTTA
1 TTATTTTTA
508071 TTATTTGTTTTA
1 TTA--T-TTTTA
*
508083 TTAATTTTA
1 TTATTTTTA
* *
508092 -TATATATA
1 TTATTTTTA
*
508100 CTATTTTT-
1 TTATTTTTA
508108 TATATTTTTA
1 T-TATTTTTA
*
508118 TTTATTATATA
1 -TTATT-TTTA
* *
508129 TATATATATA
1 T-TATTTTTA
508139 TTATTTTTA
1 TTATTTTTA
*
508148 CT-TTTTTA
1 TTATTTTTA
508156 TTA-TTTTA
1 TTATTTTTA
508164 TTTATTTGTT-
1 -TTATTT-TTA
*
508174 TTATTTATA
1 TTATTTTTA
*
508183 -TATTTTTTC
1 TTA-TTTTTA
*
508192 TTCTTTTTA
1 TTATTTTTA
508201 TTTATTTTT-
1 -TTATTTTTA
*
508210 TTATATTTTT
1 TTAT-TTTTA
508220 TTATTTT
1 TTATTTT
508227 ACTTACTATA
Statistics
Matches: 118, Mismatches: 19, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
8 24 0.20
9 52 0.44
10 24 0.20
11 10 0.08
12 8 0.07
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (9 bp):
TTATTTTTA
Found at i:508155 original size:38 final size:38
Alignment explanation
Indices: 508033--508165 Score: 130
Period size: 39 Copynumber: 3.4 Consensus size: 38
508023 TTAGTATATA
* * *
508033 TTTTTATTTTTTTATATTACATATATATTTTATTTTTAT
1 TTTTTA-TTTATTATATTATATATATATATTATTTTTAT
* *
508072 TATTTGT-TTTATTA-ATTTTATATATATACTATTTTTTAT
1 T-TTT-TATTTATTATATTATATATATATATTA-TTTTTAT
508111 ATTTTTATTTATTATA-TATATATATATATTATTTTTACT
1 -TTTTTATTTATTATATTATATATATATATTATTTTTA-T
*
508150 TTTTTA-TTATTTTATT
1 TTTTTATTTATTATATT
508166 TATTTGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 17
0.76 0.08 0.17
Matches are distributed among these distances:
37 7 0.09
38 27 0.35
39 38 0.49
40 5 0.06
41 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (38 bp):
TTTTTATTTATTATATTATATATATATATTATTTTTAT
Found at i:508183 original size:46 final size:45
Alignment explanation
Indices: 508060--508225 Score: 126
Period size: 46 Copynumber: 3.6 Consensus size: 45
508050 TACATATATA
* * * * * *
508060 TTTTATTTTTATTATTTGTTTTATTAATTT-TATATATATACTA-TT
1 TTTTATTATT-TTATTTATTTT-TTTATTTATATATTTTTTCTACTT
* * *
508105 TTTTA-TATTTTTATTTATTATATATATATATATATTATTTT-TACTT
1 TTTTATTA-TTTTATTTATT-TTTTTATTTATATATT-TTTTCTACTT
*
508151 TTTTATTATTTTATTTATTTGTTTTATTTATATATTTTTTCTTC-T
1 TTTTATTATTTTATTTATTT-TTTTATTTATATATTTTTTCTACTT
*
508196 TTTTATTTATTTTTTTATATTTTTTTATTT
1 TTTTA-TTATTTTATT-TATTTTTTTATTT
508226 TACTTACTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 19
0.75 0.11 0.15
Matches are distributed among these distances:
44 13 0.13
45 26 0.27
46 51 0.53
47 7 0.07
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (45 bp):
TTTTATTATTTTATTTATTTTTTTATTTATATATTTTTTCTACTT
Found at i:508465 original size:3 final size:3
Alignment explanation
Indices: 508457--508557 Score: 105
Period size: 3 Copynumber: 33.3 Consensus size: 3
508447 ATTATTTTAA
* * *
508457 ATT ATT ATT ATT ATT ATC AAT ATT AAT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * *
508504 ATT AAA ATT ATT ATT ATT ATT AAT ATT ATAC ATT ATAT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT
508551 ATT ATT A
1 ATT ATT A
508558 AATAATTACA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.03
3 74 0.93
4 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:508480 original size:12 final size:11
Alignment explanation
Indices: 508447--508520 Score: 55
Period size: 12 Copynumber: 6.7 Consensus size: 11
508437 TTGTTTTAAA
*
508447 ATTATTTTAA-
1 ATTATTATAAT
508457 ATTATTAT--T
1 ATTATTATAAT
508466 ATTATTATCAAT
1 ATTATTAT-AAT
* *
508478 ATTAATATATT
1 ATTATTATAAT
*
508489 ATTATTATTATT
1 ATTATTA-TAAT
*
508501 ATTATTAAAATT
1 ATTATTATAA-T
508513 ATTATTAT
1 ATTATTAT
508521 TATTAATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 8 0.16
10 7 0.14
11 9 0.18
12 27 0.53
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATTATAAT
Found at i:510005 original size:13 final size:13
Alignment explanation
Indices: 509987--510030 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
509977 TCATTGTTTA
509987 TTTATATTTTAAT
1 TTTATATTTTAAT
510000 TTTATATGTTT-AT
1 TTTATAT-TTTAAT
510013 TTTATA-TTTAAT
1 TTTATATTTTAAT
510025 TATTAT
1 T-TTAT
510031 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.11
12 3 0.11
13 19 0.68
14 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTATATTTTAAT
Found at i:510009 original size:25 final size:26
Alignment explanation
Indices: 509981--510030 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
509971 TTTCAGTCAT
509981 TGTTTA-TTTATATTTTAATT-TTATA
1 TGTTTATTTTATA-TTTAATTATTATA
510006 TGTTTATTTTATATTTAATTATTAT
1 TGTTTATTTTATATTTAATTATTAT
510031 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TGTTTATTTTATATTTAATTATTATA
Found at i:510031 original size:3 final size:3
Alignment explanation
Indices: 510023--510049 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
510013 TTTATATTTA
510023 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
510050 TAGTCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:518584 original size:75 final size:75
Alignment explanation
Indices: 518442--518613 Score: 195
Period size: 75 Copynumber: 2.3 Consensus size: 75
518432 GAAGAAGATG
* * *
518442 TTGGGGCA-GACTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGATGTATTCTGAACGTTTAT
1 TTGGGGCATG-CTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTCTGAACGCTTAT
518506 ATTAGCAAAATA
65 ATTAGC-AAATA
* ** * * *
518518 TTGGGGCATGCTGAAAG-CCTTTTTTATCAGAATCAGGAATGTTGACGCATTTTGCACGCTTGTA
1 TTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTCTGAACGCTTATA
* *
518582 TTAGCCAATG
66 TTAGCAAATA
* *
518592 TTGGGTCATGCTGAAGGCCCAT
1 TTGGGGCATGCTGAAAGCCCAT
518614 ATCATCATGT
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
74 18 0.22
75 46 0.57
76 15 0.19
77 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (75 bp):
TTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGACGCATTCTGAACGCTTATA
TTAGCAAATA
Found at i:519942 original size:22 final size:22
Alignment explanation
Indices: 519895--519991 Score: 135
Period size: 22 Copynumber: 4.5 Consensus size: 22
519885 ACATTTACCT
* *
519895 TTTTCAAAGATG--AGATACAC
1 TTTTCAAAGATGATAGATTCTC
*
519915 TATTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
*
519937 TCTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
*
519959 TTTTTAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
519981 TTTTCAAAGAT
1 TTTTCAAAGAT
519992 TAAAGCTATA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.16
22 57 0.84
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTCTC
Found at i:520585 original size:12 final size:12
Alignment explanation
Indices: 520568--520592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
520558 TTCCTAAAGA
520568 GAGGATATTAAG
1 GAGGATATTAAG
520580 GAGGATATTAAG
1 GAGGATATTAAG
520592 G
1 G
520593 TTAAAGATGA
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:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (12 bp):
GAGGATATTAAG
Found at i:520864 original size:64 final size:65
Alignment explanation
Indices: 520791--520952 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 65
520781 ATTGTTTGAC
* *** *
520791 GGTGTATCGATGCACAGGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACACCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAAT-AAACAAACACCGAATGCAAT
520854 T
65 T
* * * * *
520855 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACACCGAATGCAAT
520918 T
65 T
** *
520919 TATGCACCGATGCACAGGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAC
520953 CGACAGGGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 7 0.09
64 67 0.86
65 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (65 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACACCGAATGCAATT
Found at i:522063 original size:103 final size:103
Alignment explanation
Indices: 521735--522055 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
521725 ATCGAGGGTC
521735 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
521800 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
521838 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
521903 TTGATCCTTGGCATATGTAAATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
521941 TATATGGTCCTTCGAGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
522006 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
522044 TATGTGGTCCTT
1 TATGTGGTCCTT
522056 ATGGACATTA
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:522138 original size:23 final size:23
Alignment explanation
Indices: 522065--522138 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
522055 TATGGACATT
*
522065 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTCCGGTGCA
* *
522086 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTCCGGTGCA
* * *
522109 ATTATATGTGGCATTTCGGTGCA
1 ATTATATGCGGCACTCCGGTGCA
522132 ATTATAT
1 ATTATAT
522139 CAGCTGTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 5 0.12
23 38 0.88
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGCGGCACTCCGGTGCA
Found at i:527865 original size:102 final size:103
Alignment explanation
Indices: 527678--527996 Score: 597
Period size: 102 Copynumber: 3.1 Consensus size: 103
527668 GTCGAGGGTC
527678 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
527743 TTGATCCTTGGCATAT-TATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
527780 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGT-AGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
527844 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
527882 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
527947 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
527985 TATGTGGTCCTT
1 TATGTGGTCCTT
527997 ATGGACATTA
Statistics
Matches: 212, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
101 26 0.12
102 129 0.61
103 57 0.27
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:529987 original size:73 final size:73
Alignment explanation
Indices: 529854--530399 Score: 934
Period size: 73 Copynumber: 7.5 Consensus size: 73
529844 CTATTTCCAA
* * * *
529854 CATCCGTAAGCCCTGCAGTGCAGGATGTTTT-AAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
529918 CTCAGGGT
66 CTCAGGGT
* *
529926 CATTTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
529991 CTCAGGGT
66 CTCAGGGT
*
529999 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
530064 CTCAGGGT
66 CTCAGGGT
* * *
530072 CATCTGTAAGACCTACAATGTATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
530137 CTTAGGGT
66 CTCAGGGT
*
530145 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
530210 CTCAGGGT
66 CTCAGGGT
*
530218 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
530283 CTCAGGGT
66 CTCAGGGT
*
530291 CATCTGTAAGACCTACAGTGCATGAT-TTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
530355 CTAAGGGT
66 CTCAGGGT
*
530363 TATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAA
530400 CTTGTTCGCG
Statistics
Matches: 447, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
72 93 0.21
73 354 0.79
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:531263 original size:24 final size:24
Alignment explanation
Indices: 531219--531268 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
531209 ATAAAGAACC
*
531219 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
531243 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
531267 AA
1 AA
531269 TCAACCACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:533572 original size:20 final size:19
Alignment explanation
Indices: 533528--533579 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
533518 TGAAGGAAAG
*
533528 AGAAAAAGTAAAAGTTAAAA
1 AGAAAAAG-AAAAATTAAAA
*
533548 TGAAAAAGAAAAATTAATAA
1 AGAAAAAGAAAAATTAA-AA
*
533568 AGAAATAGAAAA
1 AGAAAAAGAAAA
533580 GAAAAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.15
Consensus pattern (19 bp):
AGAAAAAGAAAAATTAAAA
Found at i:533776 original size:16 final size:18
Alignment explanation
Indices: 533741--533777 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
533731 ATCAAAAATT
*
533741 AAATAGAAAATGAAATAA
1 AAATAGAAAATGAAAGAA
533759 AAATA-AAAAT-AAAGAA
1 AAATAGAAAATGAAAGAA
533775 AAA
1 AAA
533778 CTTAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AAATAGAAAATGAAAGAA
Found at i:538210 original size:24 final size:24
Alignment explanation
Indices: 538183--538232 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
538173 AAAAAGAACC
*
538183 AAAATAAACTT-AAATATACCATTA
1 AAAATAAACTTCAAACA-ACCATTA
*
538207 AAAATAAAGTTCAAACAACCATTA
1 AAAATAAACTTCAAACAACCATTA
538231 AA
1 AA
538233 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTCAAACAACCATTA
Found at i:539222 original size:3 final size:3
Alignment explanation
Indices: 539204--539312 Score: 89
Period size: 3 Copynumber: 36.3 Consensus size: 3
539194 TTCTTTTAAA
* * * * *
539204 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AAT A-T AGT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
539249 ATT ATT ATT ATT ATT ATT A-A ATT ATT ATT ATT ATT AAT ATAC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
*
539294 ATAT CTT ATT ATT A-T ATT A
1 AT-T ATT ATT ATT ATT ATT A
539313 AATAATTACA
Statistics
Matches: 84, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
2 5 0.06
3 73 0.87
4 6 0.07
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:539245 original size:26 final size:26
Alignment explanation
Indices: 539216--539279 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
539206 TATTTTTAAT
539216 TATTATTATTATCAATATTAATA-TA
1 TATTATTATTATCAATATTAATATTA
* * *
539241 GTATTATTATTATTATTATTATTATTA
1 -TATTATTATTATCAATATTAATATTA
*
539268 AATTATTATTAT
1 TATTATTATTAT
539280 TATTAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 31 0.94
27 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TATTATTATTATCAATATTAATATTA
Found at i:539280 original size:26 final size:26
Alignment explanation
Indices: 539204--539284 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 26
539194 TTCTTTTAAA
* *
539204 ATTATT-TTTAATTATTATTATTATC
1 ATTATTATTAAATTATTATTATTATT
* *
539229 AATATTAATATAGTATTATTATTATTATT
1 ATTATT-AT-TA-AATTATTATTATTATT
539258 ATTATTATTAAATTATTATTATTATT
1 ATTATTATTAAATTATTATTATTATT
539284 A
1 A
539285 ATATACATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
25 5 0.11
26 16 0.35
27 3 0.07
28 3 0.07
29 19 0.41
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
ATTATTATTAAATTATTATTATTATT
Found at i:539302 original size:29 final size:28
Alignment explanation
Indices: 539214--539320 Score: 116
Period size: 29 Copynumber: 3.9 Consensus size: 28
539204 ATTATTTTTA
*
539214 ATTATTATTATTATCAATATTAA-TATAGT
1 ATTATTATTATTATTAATA-TAATTATA-T
* *
539243 ATTATTATTATTATTATTATTATTA-A-
1 ATTATTATTATTATTAATATAATTATAT
539269 ATTATTATTATTATTAATATACATTATAT
1 ATTATTATTATTATTAATATA-ATTATAT
*
539298 CTTATTATTA-TATTAA-ATAATTA
1 ATTATTATTATTATTAATATAATTA
539321 CATTACAAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
26 23 0.34
27 7 0.10
28 10 0.15
29 28 0.41
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (28 bp):
ATTATTATTATTATTAATATAATTATAT
Found at i:540721 original size:13 final size:12
Alignment explanation
Indices: 540687--540729 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
540677 ATTCAGTCAT
540687 TGTTTATTTATA
1 TGTTTATTTATA
540699 T-TTTAATTTATA
1 TGTTT-ATTTATA
540711 TGTTTATTT-TA
1 TGTTTATTTATA
*
540722 TATTTATT
1 TGTTTATT
540730 ATTATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 12 0.43
12 13 0.46
13 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
TGTTTATTTATA
Found at i:540733 original size:3 final size:3
Alignment explanation
Indices: 540725--540761 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
540715 TATTTTATAT
540725 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
540762 GTATAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:540746 original size:14 final size:14
Alignment explanation
Indices: 540729--540761 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
540719 TTATATTTAT
540729 TATTATTATTATTA
1 TATTATTATTATTA
*
540743 TATTATTATTATTT
1 TATTATTATTATTA
540757 TATTA
1 TATTA
540762 GTATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:540761 original size:11 final size:11
Alignment explanation
Indices: 540713--540761 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
540703 AATTTATATG
540713 TTTATT-TTAT
1 TTTATTATTAT
540723 ATTTATTATTA-
1 -TTTATTATTAT
540734 -TTATTATTAT
1 TTTATTATTAT
*
540744 ATTATTATTAT
1 TTTATTATTAT
540755 TTTATTA
1 TTTATTA
540762 GTATAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
9 9 0.26
11 22 0.65
12 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:542177 original size:172 final size:168
Alignment explanation
Indices: 541870--542210 Score: 630
Period size: 172 Copynumber: 2.0 Consensus size: 168
541860 CGACTTCACT
541870 ACCCCAATCCAAGGGTGATCAATAGGATAATCATGATTCCGATATATACTATGTTCGTTCGGGTT
1 ACCCCAATCCAAGGGTGATCAATAGGATAATCATGATTCCGATATATACTATGTTCGTTCGGGTT
541935 AATGGTGGCTTCAACGTCCCAATCATTCTCTGACATCTGCTTCCAGAGTTCGGGAAATAGTTGAT
66 AATGGTGGCTTCAACGTCCCAATCATTCTCTGACATCTGCTTCCAGAGTTCGGGAAATAGTTGAT
542000 AAACTATAGATCCT-CCTAAGATTAAGATCTTTGCTTG
131 AAACTATAGATCCTACCTAAGATTAAGATCTTTGCTTG
542037 ACCCCAATCCAAAGGGATGTGATCATATAGGATAATCATGATTCCGATATATACTATGTTCGTTC
1 ACCCCAATCC-AA-GG--GTGATCA-ATAGGATAATCATGATTCCGATATATACTATGTTCGTTC
542102 GGGTTAATGGTGGCTTCAACGTCCCAATCATTCTCTGACATCTGCTTCCAGAGTTCGGGAAATAG
61 GGGTTAATGGTGGCTTCAACGTCCCAATCATTCTCTGACATCTGCTTCCAGAGTTCGGGAAATAG
542167 TTGATAAACTATAGATCCTACCTAAGATTAAGATCTTTGCTTG
126 TTGATAAACTATAGATCCTACCTAAGATTAAGATCTTTGCTTG
542210 A
1 A
542211 AGAGTGGTGC
Statistics
Matches: 168, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
167 10 0.06
168 2 0.01
169 2 0.01
171 7 0.04
172 123 0.73
173 24 0.14
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (168 bp):
ACCCCAATCCAAGGGTGATCAATAGGATAATCATGATTCCGATATATACTATGTTCGTTCGGGTT
AATGGTGGCTTCAACGTCCCAATCATTCTCTGACATCTGCTTCCAGAGTTCGGGAAATAGTTGAT
AAACTATAGATCCTACCTAAGATTAAGATCTTTGCTTG
Found at i:549249 original size:28 final size:29
Alignment explanation
Indices: 549218--549279 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
549208 ATCGATATAC
* *
549218 AACTAAATCG-ACTTCTGTCGTAATCTCA
1 AACTAAATCGTACTTCCGTCATAATCTCA
549246 AACTAAATCGTACTTCCGTCATAATCTCA
1 AACTAAATCGTACTTCCGTCATAATCTCA
549275 AACTA
1 AACTA
549280 CATGTTCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (29 bp):
AACTAAATCGTACTTCCGTCATAATCTCA
Found at i:552091 original size:23 final size:23
Alignment explanation
Indices: 552043--552097 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
552033 GACCGGTCAT
* **
552043 GACCCGACCCTATCCGTTGATTC
1 GACCCGACCCTACCCGTTGACCC
552066 GACCCGACCCTACCCGTTGACCC
1 GACCCGACCCTACCCGTTGACCC
*
552089 GACCAGACC
1 GACCCGACC
552098 GTTTACCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.18, T:0.16
Consensus pattern (23 bp):
GACCCGACCCTACCCGTTGACCC
Found at i:552180 original size:29 final size:28
Alignment explanation
Indices: 552120--552303 Score: 136
Period size: 29 Copynumber: 6.4 Consensus size: 28
552110 CCGTTGACCA
*** *
552120 GTGCTATTCTGGGAATTAATTCGGTTATG
1 GTGCTATT-TGGGAATTAATTCGAAAAGG
* *
552149 GTGCTATTCTAGGAATTAATTTGAAAAGG
1 GTGCTATT-TGGGAATTAATTCGAAAAGG
* ** **
552178 GTGCTATTTTGGTAATATTTTTCGAAAAAT
1 GTGCTA-TTTGGGAAT-TAATTCGAAAAGG
* **
552208 GTGATATTTTGGGAATTAATTCGAAATTG
1 GTGCTA-TTTGGGAATTAATTCGAAAAGG
552237 GTGCTATTTTGGGAATTAATTCGAAAA-G
1 GTGCTA-TTTGGGAATTAATTCGAAAAGG
* * **
552265 GTGCTATTTTGGTAATTATTTTAAAAAGG
1 GTGCTA-TTTGGGAATTAATTCGAAAAGG
552294 GTGCTATTTG
1 GTGCTATTTG
552304 TGTAAAATAT
Statistics
Matches: 126, Mismatches: 26, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
28 28 0.22
29 74 0.59
30 24 0.19
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (28 bp):
GTGCTATTTGGGAATTAATTCGAAAAGG
Found at i:552240 original size:59 final size:57
Alignment explanation
Indices: 552120--552302 Score: 168
Period size: 59 Copynumber: 3.2 Consensus size: 57
552110 CCGTTGACCA
* ** * * * * *
552120 GTGCTATTCTGGGAATTAATTCGGTTATGGTGCTATTCTAGGAATTAATTTGAAAAGG
1 GTGCTATTTTGGGAATTAATTC-GAAAAGGTGATATTTTGGGAATTAATTCGAAAAGG
* ** * **
552178 GTGCTATTTTGGTAATATTTTTCGAAAAATGTGATATTTTGGGAATTAATTCGAAATTG
1 GTGCTATTTTGGGAAT-TAATTCG-AAAAGGTGATATTTTGGGAATTAATTCGAAAAGG
* * * **
552237 GTGCTATTTTGGGAATTAATTCGAAAAGGTGCTATTTTGGTAATTATTTTAAAAAGG
1 GTGCTATTTTGGGAATTAATTCGAAAAGGTGATATTTTGGGAATTAATTCGAAAAGG
552294 GTGCTATTT
1 GTGCTATTT
552303 GTGTAAAATA
Statistics
Matches: 98, Mismatches: 25, Indels: 5
0.77 0.20 0.04
Matches are distributed among these distances:
57 35 0.36
58 20 0.20
59 43 0.44
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.42
Consensus pattern (57 bp):
GTGCTATTTTGGGAATTAATTCGAAAAGGTGATATTTTGGGAATTAATTCGAAAAGG
Found at i:552285 original size:88 final size:88
Alignment explanation
Indices: 552124--552286 Score: 240
Period size: 88 Copynumber: 1.9 Consensus size: 88
552114 TGACCAGTGC
** *
552124 TATTCTGGGAATTAATTCGGTTATGGTGCTATTCTAGGAATTAATTTGAAAAGGGTGCTATTTTG
1 TATTCTGGGAATTAATTCGAATATGGTGCTATTCTAGGAATTAATTCGAAAAGGGTGCTATTTTG
552189 GTAATATTTTTCGAAAAATGTGA
66 GTAATATTTTTCGAAAAATGTGA
* * *
552212 TATTTTGGGAATTAATTCGAA-ATTGGTGCTATTTTGGGAATTAATTCGAAAA-GGTGCTATTTT
1 TATTCTGGGAATTAATTCGAATA-TGGTGCTATTCTAGGAATTAATTCGAAAAGGGTGCTATTTT
552275 GGTAATTATTTT
65 GGTAA-TATTTT
552287 AAAAAGGGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 17 0.25
88 50 0.75
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (88 bp):
TATTCTGGGAATTAATTCGAATATGGTGCTATTCTAGGAATTAATTCGAAAAGGGTGCTATTTTG
GTAATATTTTTCGAAAAATGTGA
Found at i:553220 original size:42 final size:41
Alignment explanation
Indices: 553161--553491 Score: 457
Period size: 42 Copynumber: 7.8 Consensus size: 41
553151 GAAGTATTAT
553161 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
553203 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
*
553245 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* * *
553287 TAGGTCCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
*
553329 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
553371 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
553413 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTTTC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTAC
* *
553455 CTAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 C-AGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
553492 TGGTGTATAG
Statistics
Matches: 261, Mismatches: 19, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
41 8 0.03
42 221 0.85
43 20 0.08
44 12 0.05
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:553303 original size:84 final size:84
Alignment explanation
Indices: 553161--553491 Score: 531
Period size: 84 Copynumber: 3.9 Consensus size: 84
553151 GAAGTATTAT
*
553161 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
553226 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
* *
553245 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTACTAGGTCCCTTTTCTGTGTGCAAG
1 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
553310 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
553329 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
553394 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
* * * * *
553413 CAGGTCCCTTTGCTGTGTGC-AAGGATAAACCTTACAGTTTTCCTAGG-CTCCTCTGCTTTGTGC
1 CAGGTCCCTTTGATGTGTGCGAAGG-TAAGCCTTACAGTTTACC-AGGTC-CCTTTGCTGTGTGC
*
553476 ACAGGTTAAGCCTTAC
63 A-AGGGTAAGCCTTAC
553492 TGGTGTATAG
Statistics
Matches: 232, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
83 4 0.02
84 199 0.86
85 16 0.07
86 13 0.06
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (84 bp):
CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
GGTAAGCCTTACAGTTTCC
Found at i:553834 original size:16 final size:16
Alignment explanation
Indices: 553813--553843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
553803 CGTTGTGGAC
*
553813 TTATCTGTATTATATA
1 TTATCTATATTATATA
553829 TTATCTATATTATAT
1 TTATCTATATTATAT
553844 TAACGTTCTA
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:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATCTATATTATATA
Found at i:559601 original size:18 final size:18
Alignment explanation
Indices: 559580--559614 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
559570 TCATGACCAG
559580 ACCCGTTGACCCGACCCT
1 ACCCGTTGACCCGACCCT
559598 ACCCGTTGACCCGACCC
1 ACCCGTTGACCCGACCC
559615 GACGACCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.51, G:0.17, T:0.14
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCT
Found at i:559614 original size:31 final size:31
Alignment explanation
Indices: 559573--559639 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
559563 TGACATGTCA
** *
559573 TGACCAGACCCGTTGACCCGACCCTACCCGT
1 TGACCAGACCCGACGACCCAACCCTACCCGT
*
559604 TGACCCGACCCGACGACCCAACCCTACCCGT
1 TGACCAGACCCGACGACCCAACCCTACCCGT
559635 TGACC
1 TGACC
559640 GTTGACCGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.48, G:0.18, T:0.13
Consensus pattern (31 bp):
TGACCAGACCCGACGACCCAACCCTACCCGT
Found at i:559708 original size:29 final size:29
Alignment explanation
Indices: 559647--559781 Score: 130
Period size: 29 Copynumber: 4.7 Consensus size: 29
559637 ACCGTTGACC
* **
559647 GGTGCTATTATGGGAATTAATTC-AGTTTT
1 GGTGCTATTTTGGGAATTAATTCGA-AATT
*
559676 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATT
* * **
559705 GGTGCTATTTTGGTAATT-TTTCCGAAAAA
1 GGTGCTATTTTGGGAATTAATT-CGAAATT
* * *
559734 GGTGATATTCTGGGAATTAATTTGAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAATT
*
559763 GGTGCTATTTTGGTAATTA
1 GGTGCTATTTTGGGAATTA
559782 TTTTAAAAAG
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
28 2 0.02
29 80 0.94
30 3 0.04
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATT
Found at i:560704 original size:42 final size:42
Alignment explanation
Indices: 560645--560936 Score: 437
Period size: 42 Copynumber: 7.0 Consensus size: 42
560635 GAAGTATTAT
*
560645 CAGGTCCCTTTGCTGTGTGCGATGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
*
560687 CAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTAC
*
560729 CAGGTCCCTTTGCTGTGTGCGAAGGCAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
* *
560771 CAGGTCCCTTTTCTGTGTGC-AAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTAC
* *
560813 CAGGTCCCTTTGCTGTGTGCGAAGATCAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
* *
560855 CAGGTCCCTTTGCTGTGTGCCAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
* *
560897 CAGATCCCTTTGCTGTGTGC-AAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTT
560937 TCCTAGGCTC
Statistics
Matches: 228, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
41 7 0.03
42 217 0.95
43 4 0.02
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (42 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
Found at i:574767 original size:38 final size:37
Alignment explanation
Indices: 574725--574845 Score: 117
Period size: 38 Copynumber: 3.3 Consensus size: 37
574715 AGTTGGAAAA
574725 TTCATCTTTGGTAGGTGGTCAACTTTGCACATGGGAAT
1 TTCATCTTTGGTAGGTGG-CAACTTTGCACATGGGAAT
* * * * *
574763 TTCATC-TTGTTTGGTGGCCAAC-TT--A-TTGGAAAA
1 TTCATCTTTGGTAGGTGG-CAACTTTGCACATGGGAAT
* *
574796 TTCATCTTTGGTAAGTGGCAAACTTTGCACATGTGAAT
1 TTCATCTTTGGTAGGTGGC-AACTTTGCACATGGGAAT
574834 TTCATCTTTGGT
1 TTCATCTTTGGT
574846 CCCTAAAATA
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
33 12 0.19
34 12 0.19
35 2 0.03
36 2 0.03
37 14 0.22
38 22 0.34
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (37 bp):
TTCATCTTTGGTAGGTGGCAACTTTGCACATGGGAAT
Found at i:574785 original size:37 final size:37
Alignment explanation
Indices: 574725--574841 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 37
574715 AGTTGGAAAA
*
574725 TTCATCTTTGGTAGGTGGTCAACTTTGCACATGGGAAT
1 TTCATC-TTGGTAGGTGGCCAACTTTGCACATGGGAAT
* * * * *
574763 TTCATCTTGTTTGGTGGCCAAC-TT--A-TTGGAAAA
1 TTCATCTTGGTAGGTGGCCAACTTTGCACATGGGAAT
* * *
574796 TTCATCTTTGGTAAGTGGCAAACTTTGCACATGTGAAT
1 TTCATC-TTGGTAGGTGGCCAACTTTGCACATGGGAAT
574834 TTCATCTT
1 TTCATCTT
574842 TGGTCCCTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
33 11 0.18
34 13 0.22
35 2 0.03
36 2 0.03
37 16 0.27
38 16 0.27
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (37 bp):
TTCATCTTGGTAGGTGGCCAACTTTGCACATGGGAAT
Found at i:578956 original size:20 final size:20
Alignment explanation
Indices: 578908--578963 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
578898 ATGTGAAATT
* *
578908 TGTCCCGAATGACTTATGTA
1 TGTCCCGAAGGACCTATGTA
*
578928 TACGTCCCGAAGGACCTCTGTA
1 T--GTCCCGAAGGACCTATGTA
578950 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
578964 ACTATCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:579070 original size:31 final size:32
Alignment explanation
Indices: 578985--579090 Score: 153
Period size: 32 Copynumber: 3.3 Consensus size: 32
578975 GTTCCAAAGA
*
578985 ACATAGGTAACACTGTCCATATGTCCCGAATA
1 ACATAGGTAACACTGTCCATATGTCCCGAATG
579017 ACATAGGTAATC-CTGTCCATATGTCCCGAATG
1 ACATAGGTAA-CACTGTCCATATGTCCCGAATG
* * *
579049 ACATAGGTAA-ACTATCCATATGTCTCGAAAG
1 ACATAGGTAACACTGTCCATATGTCCCGAATG
579080 ACATAGGTAAC
1 ACATAGGTAAC
579091 CCTCGACTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
31 27 0.40
32 39 0.58
33 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (32 bp):
ACATAGGTAACACTGTCCATATGTCCCGAATG
Found at i:579557 original size:16 final size:16
Alignment explanation
Indices: 579536--579570 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
579526 TATAATTGAT
*
579536 CATATATAGTATGTAA
1 CATATATAGTATGCAA
579552 CATATATAGTATGCAA
1 CATATATAGTATGCAA
579568 CAT
1 CAT
579571 GTATGGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (16 bp):
CATATATAGTATGCAA
Found at i:583220 original size:31 final size:31
Alignment explanation
Indices: 583114--583240 Score: 125
Period size: 32 Copynumber: 4.0 Consensus size: 31
583104 CCCGAAGGAC
*
583114 CACTATCCATATGTTCC-AAAAACATAGGTAA
1 CACTATCCATATG-TCCGAAAGACATAGGTAA
* * *
583145 CACTGTCCATGTGTCCTGAAGGACATAGGTAA
1 CACTATCCATATGTCC-GAAAGACATAGGTAA
* * *
583177 TC-CTGTCCATATGTTCCGAAGGACATATGTAA
1 -CACTATCCATATG-TCCGAAAGACATAGGTAA
583209 -ACTATCCATATGTCTCGAAAGACATAGGTAA
1 CACTATCCATATGTC-CGAAAGACATAGGTAA
583240 C
1 C
583241 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
30 5 0.06
31 35 0.44
32 36 0.45
33 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
CACTATCCATATGTCCGAAAGACATAGGTAA
Found at i:583233 original size:63 final size:63
Alignment explanation
Indices: 583119--583239 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
583109 AGGACCACTA
* * *
583119 TCCATATGTTCCAAAAACATAGGTAACACTGTCCATGTGTCCTGAAGGACATAGGTAATCCTG
1 TCCATATGTTCCAAAAACATAGGTAACACTATCCATATGTCCTGAAAGACATAGGTAATCCTG
** *
583182 TCCATATGTTCCGAAGGACATATGTAA-ACTATCCATATGT-CTCGAAAGACATAGGTAA
1 TCCATATGTTCC-AAAAACATAGGTAACACTATCCATATGTCCT-GAAAGACATAGGTAA
583240 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.04
63 37 0.74
64 11 0.22
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (63 bp):
TCCATATGTTCCAAAAACATAGGTAACACTATCCATATGTCCTGAAAGACATAGGTAATCCTG
Found at i:586255 original size:36 final size:37
Alignment explanation
Indices: 586215--586330 Score: 118
Period size: 36 Copynumber: 3.3 Consensus size: 37
586205 TATCTTTGGA
586215 GGTGGCCAACTTTGTACATGAGAAATT-ATCTTGGTT
1 GGTGGCCAACTTTGTACATGAGAAATTCATCTTGGTT
* * *
586251 GGTGGCCAAC--T-TA-TTGAAAAATTCATCTTTGGTA
1 GGTGGCCAACTTTGTACATGAGAAATTCATC-TTGGTT
* * * *
586285 GGTGG-CAACTTTGCACATGGGAATTTCATCTTGTTT
1 GGTGGCCAACTTTGTACATGAGAAATTCATCTTGGTT
586321 GGTGGCCAAC
1 GGTGGCCAAC
586331 ATTGGAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
32 8 0.13
33 9 0.14
34 11 0.17
35 1 0.02
36 20 0.32
37 14 0.22
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (37 bp):
GGTGGCCAACTTTGTACATGAGAAATTCATCTTGGTT
Found at i:586374 original size:66 final size:68
Alignment explanation
Indices: 586198--586382 Score: 200
Period size: 69 Copynumber: 2.7 Consensus size: 68
586188 TGGCAAGTTG
* ** * * *
586198 GAAAATTTATCTTTGG-AGGTGGCCAACTTTGTACATGAGAAATT-ATCTTGGTTGGTGGCCAAC
1 GAAAAATTATCTTTGGTAGGT-GAAAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCCAAC
586261 TTATT
65 -TATT
** *
586266 GAAAAATTCATCTTTGGTAGGTGGCAACTTTGCACATGGGAATTTCATCTTGTTTGGTGGCCAAC
1 GAAAAATT-ATCTTTGGTAGGTGAAAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCCAAC
586331 -ATT
65 TATT
* *
586334 GGAAAA-T-TCTTTGGTGGGTGAAAAACTTTGCACATGGGAATTTCATCTT
1 GAAAAATTATCTTTGGTAGGTG-AAAACTTTGCACATGGGAATTTCATCTT
586383 TGGTCCCTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
65 12 0.12
66 26 0.25
67 1 0.01
68 15 0.15
69 27 0.26
70 22 0.21
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (68 bp):
GAAAAATTATCTTTGGTAGGTGAAAACTTTGCACATGGGAATTTCATCTTGGTTGGTGGCCAACT
ATT
Found at i:594140 original size:21 final size:22
Alignment explanation
Indices: 594116--594159 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
594106 AAACATTTTC
*
594116 TTAAGATAATAA-AAATTTATT
1 TTAACATAATAAGAAATTTATT
* *
594137 TTAACATAGTAAGATATTTATT
1 TTAACATAATAAGAAATTTATT
594159 T
1 T
594160 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (22 bp):
TTAACATAATAAGAAATTTATT
Found at i:594462 original size:13 final size:13
Alignment explanation
Indices: 594440--594509 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
594430 AAATAATAAT
594440 TTAAACATATAAAA
1 TTAAA-ATATAAAA
594454 TTAAAATATAAATA
1 TTAAAATATAAA-A
*
594468 ATAAAAT-TAAATA
1 TTAAAATATAAA-A
*
594481 TAAAAATAATAAAA
1 TTAAAAT-ATAAAA
*
594495 CTTATAAT-TAAAA
1 -TTAAAATATAAAA
594508 TT
1 TT
594510 GGTGACTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
12 2 0.04
13 23 0.49
14 13 0.28
15 9 0.19
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAATATAAAA
Found at i:594465 original size:21 final size:20
Alignment explanation
Indices: 594441--594507 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
594431 AATAATAATT
*
594441 TAAACATATAAAATTAAA-A
1 TAAAAATATAAAATTAAATA
*
594460 TATAAATAATAAAATTAAATA
1 TAAAAAT-ATAAAATTAAATA
594481 TAAAAATAATAAAACTTATAAT-
1 TAAAAAT-ATAAAA-TTA-AATA
594503 TAAAA
1 TAAAA
594508 TTGGTGACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.12
20 11 0.27
21 14 0.34
22 8 0.20
23 3 0.07
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAATATAAAATTAAATA
Found at i:594508 original size:21 final size:21
Alignment explanation
Indices: 594448--594507 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
594438 ATTTAAACAT
*
594448 ATAAAATTAAA-ATATAAATA
1 ATAAAATTAAATATAAAAATA
594468 ATAAAATTAAATATAAAAATA
1 ATAAAATTAAATATAAAAATA
594489 ATAAAACTTATAAT-TAAAA
1 ATAAAA-TTA-AATATAAAA
594508 TTGGTGACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 11 0.31
21 14 0.39
22 8 0.22
23 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAATTAAATATAAAAATA
Found at i:595801 original size:21 final size:21
Alignment explanation
Indices: 595776--595828 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
595766 GGTCCTGTAT
595776 TTATTAATAATAAAATAATAA
1 TTATTAATAATAAAATAATAA
* * *
595797 TTATTATTATTATAATAATAA
1 TTATTAATAATAAAATAATAA
*
595818 -TATAAATAATA
1 TTATTAATAATA
595829 TTTAAATGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATTAATAATAAAATAATAA
Found at i:596616 original size:339 final size:339
Alignment explanation
Indices: 596141--596808 Score: 966
Period size: 339 Copynumber: 2.0 Consensus size: 339
596131 CTTCTTATGC
*
596141 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
* * * *
596206 ATGAACTTCTCTGGAAAAGATGATCCATTGAATAATGAATTCAAATAAAAGGTTTGACCAAATTT
66 ATGAACTTCTCTGGAAAAGATGATCCATCGAATAATGAATTCAAAGAAAAGGTTTGAACAAATTA
* * * ***
596271 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGCTATTCTCATTATGAACTTGACCTGGAA
* ** *
596336 AAGATGATCCATCAAATGATGGATTTGAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTT
196 AAGATGATCCATCAAATGATGAATTCAAGCGAAAA-GTTGAACAAATTCTTCTCATTATGAACTT
* *
596400 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGGTCCATCGAA
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATACTGATCCATCGAA
596465 TGATGAATTCAAGCG
325 TGATGAATTCAAGCG
* *
596480 AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCAT
* * * ** *
596544 TATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAA-G-TTGAACAAG
65 TATGAACT-TCTCTGGAAAAGATGATCCATCGAATAATGAATTC-AAAGAAAAGGTTTGAACAAA
*
596607 TTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGCTATTCTCATTATGAACTTGACCTG
128 TTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGCTATTCTCATTATGAACTTGACCTG
* * * * *
596672 GCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAC
193 GAAAAGATGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAAC
* * *
596737 TTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGACCTGGCAATATTGATCCATCG
258 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATACTGATCCATCG
596802 AATGATG
323 AATGATG
596809 GATTTGAATC
Statistics
Matches: 291, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
338 35 0.12
339 215 0.74
340 36 0.12
341 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (339 bp):
AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
ATGAACTTCTCTGGAAAAGATGATCCATCGAATAATGAATTCAAAGAAAAGGTTTGAACAAATTA
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGCTATTCTCATTATGAACTTGACCTGGAA
AAGATGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATACTGATCCATCGAAT
GATGAATTCAAGCG
Found at i:596783 original size:113 final size:114
Alignment explanation
Indices: 596141--596808 Score: 861
Period size: 113 Copynumber: 5.9 Consensus size: 114
596131 CTTCTTATGC
* * *
596141 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTC-TCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * **
596205 TATGAACTTC--TCTGGAAAAGATGATCCATTGAATAATGAATTCAA-AT
66 TATGAAC-TCGACCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCG
* * * *
596252 AAAAGGTTTGACCAAATTTTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * * **
596317 TTATGAACTTTTTCTGGAAAAGATGATCCATCAAATGATGGATTTGAGC-
65 TTATGAACTCGACCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCG
* *
596366 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
596431 TATGAACTCGACCTGGCAATGCTGGTCCATCGAATGATGAATTCAAGCG
66 TATGAACTCGACCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCG
596480 AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
596544 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCG
66 TATGAACTCGAC-CTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCG
* * * *
596593 AAAA-GTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGCTATTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
596657 TATGAACTTGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCG
66 TATGAACTCGACCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCG
* *
596706 AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
596770 TATGAACTCGACCTGGCAATA-TTGATCCATCGAATGATG
66 TATGAACTCGACCTGG-AAAAGTTGATCCATCGAATGATG
596809 GATTTGAATC
Statistics
Matches: 492, Mismatches: 56, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
111 6 0.01
112 32 0.07
113 413 0.84
114 41 0.08
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (114 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGACCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCG
Found at i:597240 original size:22 final size:22
Alignment explanation
Indices: 597215--597269 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
597205 GATAAAGCTT
*
597215 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATATA
* * *
597237 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATATA
597259 TCATCTTTGAA
1 TCATCTTTGAA
597270 GAAGTAGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:599774 original size:114 final size:114
Alignment explanation
Indices: 599574--599796 Score: 374
Period size: 114 Copynumber: 2.0 Consensus size: 114
599564 GATCATGCAG
* * *
599574 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
599639 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
599688 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
599753 ACACTTCCAAAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
599797 TCATATGGCA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:601963 original size:17 final size:18
Alignment explanation
Indices: 601941--601993 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
601931 TTTCTCCTTT
601941 TTTTTTC-CTTTTTTTTC
1 TTTTTTCTCTTTTTTTTC
*
601958 TTTTTTCTTTTTTTTTTC
1 TTTTTTCTCTTTTTTTTC
*
601976 TTTTTGT-TGTTTTTTTTC
1 TTTTT-TCTCTTTTTTTTC
601994 AAGTATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 7 0.22
18 24 0.75
19 1 0.03
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTTTC
Found at i:601972 original size:27 final size:27
Alignment explanation
Indices: 601937--601990 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
601927 TCAATTTCTC
*
601937 CTTTTTTTTTCCTTTTTTTTCTTTTTT
1 CTTTTTTTTTCCTTTTTGTTCTTTTTT
* *
601964 CTTTTTTTTTTCTTTTTGTTGTTTTTT
1 CTTTTTTTTTCCTTTTTGTTCTTTTTT
601991 TTCAAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (27 bp):
CTTTTTTTTTCCTTTTTGTTCTTTTTT
Found at i:605504 original size:14 final size:14
Alignment explanation
Indices: 605471--605524 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
605461 ATGACATAAA
* *
605471 AAATGCAAAGATGCC
1 AAATGTAAATATG-C
605486 AAATGTAAATATGC
1 AAATGTAAATATGC
* *
605500 AAATGTAAAAATGT
1 AAATGTAAATATGC
605514 AAATGTAAATA
1 AAATGTAAATA
605525 CAAACGTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (14 bp):
AAATGTAAATATGC
Found at i:607682 original size:21 final size:22
Alignment explanation
Indices: 607658--607701 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
607648 AAACATTTTC
607658 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
607679 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
607701 T
1 T
607702 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:608018 original size:16 final size:17
Alignment explanation
Indices: 607988--608021 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
607978 TTATTTAAAC
607988 ATAAAATTAAAATATAA
1 ATAAAATTAAAATATAA
608005 ATAAAATT-AAATATAA
1 ATAAAATTAAAATATAA
608021 A
1 A
608022 AAGTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATTAAAATATAA
Found at i:609986 original size:12 final size:12
Alignment explanation
Indices: 609969--609994 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
609959 CATAAAGATA
609969 TTAATGTAAGAG
1 TTAATGTAAGAG
609981 TTAATGTAAGAG
1 TTAATGTAAGAG
609993 TT
1 TT
609995 TTTCTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (12 bp):
TTAATGTAAGAG
Found at i:615024 original size:200 final size:201
Alignment explanation
Indices: 614661--615063 Score: 774
Period size: 200 Copynumber: 2.0 Consensus size: 201
614651 CAACTGAGGT
614661 AACAACTGTGGACTGATTGTTGACAGAAGCCAGGACGCAAGAGCACTGTCCTGAGCTATATATTC
1 AACAACTGTGGACTGATTGTTGACAGAAGCCAGGACGCAAGAGCACTGTCCTGAGCTATATATTC
614726 TTCATATAACTCGTTCATACCTCCTCACCAGAATCACTAACCACCGTTTGGGACAGAGCAGTCAT
66 TTCATATAACTCGTTCATACCTCCTCACCAGAATCACTAACCACCGTTTGGGACAGAGCAGTCAT
614791 GGAGCCAGTGAGAAGTCGTTCAAGTCTATGGCTGCGAACGGTGAGAAGCACCTGTTGCTT-C-CA
131 GGAGCCAGTGAGAAGTCGTTCAAGTCTATGGCTGCGAACGGTGAGAAGCACCTGTTGCTTCCACA
614854 ACAGAA
196 ACAGAA
614860 AACAACTGTGGACTGATTGTTGACAGAAGCCAGGACGCAAGAGCACTGTCCTGAGCTATATATTC
1 AACAACTGTGGACTGATTGTTGACAGAAGCCAGGACGCAAGAGCACTGTCCTGAGCTATATATTC
*
614925 TTCATATAACTCGTTCAATACCTCCTCACCAGAATCACTAACCACCGTTTGTGACAGAGCAGTCA
66 TTCATATAACTCGTTC-ATACCTCCTCACCAGAATCACTAACCACCGTTTGGGACAGAGCAGTCA
614990 TGGAGCCAGTGAGAAGTCGTTCAAGTCTATGGCTGCGAACGGTGAGAAGCACCTGTTGCTTCCAC
130 TGGAGCCAGTGAGAAGTCGTTCAAGTCTATGGCTGCGAACGGTGAGAAGCACCTGTTGCTTCCAC
615055 AACAGAA
195 AACAGAA
615062 AA
1 AA
615064 TTTGATTCAT
Statistics
Matches: 200, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
199 81 0.41
200 108 0.54
201 1 0.00
202 10 0.05
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (201 bp):
AACAACTGTGGACTGATTGTTGACAGAAGCCAGGACGCAAGAGCACTGTCCTGAGCTATATATTC
TTCATATAACTCGTTCATACCTCCTCACCAGAATCACTAACCACCGTTTGGGACAGAGCAGTCAT
GGAGCCAGTGAGAAGTCGTTCAAGTCTATGGCTGCGAACGGTGAGAAGCACCTGTTGCTTCCACA
ACAGAA
Found at i:640978 original size:31 final size:31
Alignment explanation
Indices: 640943--641001 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
640933 TATTAACGAC
640943 TGTAAAAAAGTGATTGA-TCTTTAATTGTTAA
1 TGTAAAAAAGTGATTGAGT-TTTAATTGTTAA
* **
640974 TGTAACAGGGTGATTGAGTTTTAATTGT
1 TGTAAAAAAGTGATTGAGTTTTAATTGT
641002 CAGATGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.42
Consensus pattern (31 bp):
TGTAAAAAAGTGATTGAGTTTTAATTGTTAA
Found at i:641567 original size:30 final size:30
Alignment explanation
Indices: 641491--641595 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 30
641481 TCTATGTAAC
*
641491 TTAATAAAAATATTTAATAT-ATTATTTATAT
1 TTAA-AAAAATATTTAATATGA-TATTTGTAT
** * *
641522 TT-TTAAAATAGTTAATCTGATATTTGTAT
1 TTAAAAAAATATTTAATATGATATTTGTAT
* * *
641551 TTAAAAAAATATTTAATGTGATGTTCGTATT
1 TTAAAAAAATATTTAATATGATATTTGTA-T
*
641582 TTAAGAAAATATTT
1 TTAAAAAAATATTT
641596 GATTTGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
29 22 0.37
30 21 0.36
31 16 0.27
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (30 bp):
TTAAAAAAATATTTAATATGATATTTGTAT
Found at i:641591 original size:31 final size:30
Alignment explanation
Indices: 641526--641595 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
641516 TTATATTTTT
* *
641526 AAAATAGTTAATCTGATATTTGTATTTAAA
1 AAAATATTTAATCTGATATTCGTATTTAAA
* * *
641556 AAAATATTTAATGTGATGTTCGTATTTTAAG
1 AAAATATTTAATCTGATATTCGTA-TTTAAA
641587 AAAATATTT
1 AAAATATTT
641596 GATTTGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (30 bp):
AAAATATTTAATCTGATATTCGTATTTAAA
Found at i:641832 original size:28 final size:29
Alignment explanation
Indices: 641800--641890 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 29
641790 GGTTATTATA
* * * *
641800 TTAAAA-TACATGTATCACACTAGACAAT
1 TTAAAACTACATGTATTAAATTAGACATT
* * * *
641828 TTAAAATTATATGCATTATATTAGACATT
1 TTAAAACTACATGTATTAAATTAGACATT
641857 TTAAAACTACATGTATTAAATTAGACATT
1 TTAAAACTACATGTATTAAATTAGACATT
641886 TTAAA
1 TTAAA
641891 GATATAAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 6 0.12
29 46 0.88
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAAAACTACATGTATTAAATTAGACATT
Found at i:641902 original size:29 final size:29
Alignment explanation
Indices: 641842--641903 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
641832 AATTATATGC
* **
641842 ATTATATTAGACATTTTAAAACTACATGT
1 ATTAAATTAGACATTTTAAAACTACAAAT
*
641871 ATTAAATTAGACATTTTAAAGA-TATAAAT
1 ATTAAATTAGACATTTTAAA-ACTACAAAT
641900 ATTA
1 ATTA
641904 CATTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (29 bp):
ATTAAATTAGACATTTTAAAACTACAAAT
Found at i:645444 original size:17 final size:18
Alignment explanation
Indices: 645424--645457 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
645414 TAACTTACAT
645424 TTAACTTT-AACTCAATA
1 TTAACTTTAAACTCAATA
*
645441 TTAATTTTAAACTCAAT
1 TTAACTTTAAACTCAAT
645458 CTATTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAACTTTAAACTCAATA
Found at i:645621 original size:29 final size:29
Alignment explanation
Indices: 645553--645645 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 29
645543 AATATATATA
*
645553 ATTTAAGAAAATAATTAATAT-ATTATTTAT
1 ATTTAA-AAAATAATTAATATGA-TATTTGT
* *
645583 ATATT-TAAAATAGTTAATATGATATTTGT
1 AT-TTAAAAAATAATTAATATGATATTTGT
* * * *
645612 ATTTAAAAAAATATTTAATGTGATGTTCGT
1 ATTT-AAAAAATAATTAATATGATATTTGT
645642 ATTT
1 ATTT
645646 TGAGAATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.04
29 21 0.41
30 26 0.51
31 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (29 bp):
ATTTAAAAAATAATTAATATGATATTTGT
Found at i:645630 original size:30 final size:30
Alignment explanation
Indices: 645589--645645 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
645579 TTATATATTT
*
645589 AAAATAGTTAATATGATATTTGTATTTAAA
1 AAAATAGTTAATATGATATTCGTATTTAAA
* * *
645619 AAAATATTTAATGTGATGTTCGTATTT
1 AAAATAGTTAATATGATATTCGTATTT
645646 TGAGAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (30 bp):
AAAATAGTTAATATGATATTCGTATTTAAA
Found at i:645888 original size:29 final size:29
Alignment explanation
Indices: 645856--645929 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
645846 ACATGTATCG
* * * *
645856 TATTGGACAATTTAAAATTATATGCATTA
1 TATTAGACATTTTAAAAGTACATGCATTA
*
645885 TATTAGACATTTTAAAAGTACATGTATTA
1 TATTAGACATTTTAAAAGTACATGCATTA
*
645914 AATTAGACATTTTAAA
1 TATTAGACATTTTAAA
645930 GATATAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (29 bp):
TATTAGACATTTTAAAAGTACATGCATTA
Found at i:645941 original size:29 final size:29
Alignment explanation
Indices: 645881--645942 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
645871 AATTATATGC
* **
645881 ATTATATTAGACATTTTAAAAGTACATGT
1 ATTAAATTAGACATTTTAAAAGTACAAAT
*
645910 ATTAAATTAGACATTTT-AAAGATATAAAT
1 ATTAAATTAGACATTTTAAAAG-TACAAAT
645939 ATTA
1 ATTA
645943 CATTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (29 bp):
ATTAAATTAGACATTTTAAAAGTACAAAT
Found at i:651014 original size:74 final size:74
Alignment explanation
Indices: 650893--651035 Score: 241
Period size: 74 Copynumber: 1.9 Consensus size: 74
650883 GGATGAATTT
*
650893 ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGTTGCTATA
1 ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGCTGCTATA
650958 ACAATTTTC
66 ACAATTTTC
* * * *
650967 ATCAGCATAAAATAGATATTAACGCTGGAATTGCAGCAGACACAACTGTATTACCAGCTGCTGTA
1 ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGCTGCTATA
651032 ACAA
66 ACAA
651036 CTAAAAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (74 bp):
ATCAGCATAAAATAGATATTAACGATGGAATCGCAGCAGACACAACTGTATTAACAGCTGCTATA
ACAATTTTC
Found at i:652354 original size:21 final size:21
Alignment explanation
Indices: 652328--652377 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
652318 CTGCGATGGT
652328 CGCAATAGTGTCCGCAACGGC
1 CGCAATAGTGTCCGCAACGGC
* *
652349 CGCAATAGTGTCCGCGACGGG
1 CGCAATAGTGTCCGCAACGGC
*
652370 CGCTATAG
1 CGCAATAG
652378 CGCCCGCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (21 bp):
CGCAATAGTGTCCGCAACGGC
Found at i:657077 original size:59 final size:60
Alignment explanation
Indices: 657000--657167 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 60
656990 AATATGATAA
* * *
657000 TTTGTTGAAT-TCGCGACTATTAAAAGTTACAAAATGATCTTCCGACTATAGGGCATTGC
1 TTTGTTGAGTCTCGCGACTATTAAAAGTTACAAAATGATCATCCGACTATAAGGCATTGC
* ** **
657059 TTTGTTGAGTCTC-CGACTATTAAAAGTTACAAAATGATCCTCTTACTATAAGGTGTTGC
1 TTTGTTGAGTCTCGCGACTATTAAAAGTTACAAAATGATCATCCGACTATAAGGCATTGC
* * *
657118 TTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATGATCACCCGACTAT
1 TTTGTTGAGTCTCGCGACTATTAAAAGTTACAAAATGATCATCCGACTAT
657168 TCATATATCC
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 61 0.64
60 34 0.36
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (60 bp):
TTTGTTGAGTCTCGCGACTATTAAAAGTTACAAAATGATCATCCGACTATAAGGCATTGC
Found at i:659869 original size:27 final size:27
Alignment explanation
Indices: 659812--659869 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
659802 GTATAACGTT
* *
659812 AAAAATATTAGACACCTGAATTGATAG
1 AAAAATATTAGACACCTGAAATGATAA
659839 AAAAATAGTTAAGACACCT-AAATG-TAA
1 AAAAATA-TT-AGACACCTGAAATGATAA
659866 AAAA
1 AAAA
659870 TGTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 13 0.48
28 6 0.22
29 8 0.30
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (27 bp):
AAAAATATTAGACACCTGAAATGATAA
Found at i:665585 original size:20 final size:20
Alignment explanation
Indices: 665560--665629 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
665550 TAGGTGAGTC
665560 GTATCGATACTGTTATTACA
1 GTATCGATACTGTTATTACA
* * *
665580 GTATCGATACCG-CATGAACA
1 GTATCGATACTGTTAT-TACA
* * * *
665600 ATATCGATATTGTTCTTGCA
1 GTATCGATACTGTTATTACA
665620 GTATCGATAC
1 GTATCGATAC
665630 CAAAGGTAAG
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 2 0.06
20 33 0.92
21 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (20 bp):
GTATCGATACTGTTATTACA
Found at i:669717 original size:17 final size:18
Alignment explanation
Indices: 669689--669728 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
669679 CATACTAATT
669689 TTTTTGTAATTTTTCTGA
1 TTTTTGTAATTTTTCTGA
669707 TTTTTGT-ATTTTTCTGA
1 TTTTTGTAATTTTTCTGA
669724 TTTTT
1 TTTTT
669729 TTAAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTTTGTAATTTTTCTGA
Found at i:669729 original size:18 final size:19
Alignment explanation
Indices: 669688--669729 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
669678 ACATACTAAT
669688 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
669707 -TTTTTGT-ATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
669724 TTTTTT
1 TTTTTT
669730 TAAATTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTTTGTAATTTTTCTGA
Found at i:669795 original size:105 final size:106
Alignment explanation
Indices: 669607--669849 Score: 332
Period size: 105 Copynumber: 2.3 Consensus size: 106
669597 AACGCTACAA
* **
669607 TTTTCTG-TTTTTTT-AATTCAAATAGATTAAATTAAAAGATATATAAAAATACATTGAAATTAA
1 TTTTCTGATTTTTTTAAATTCAAATAGATTAATTTGCAAG----ATAAAAATA-ATTGAAATTAA
* *
669670 ATATATAAACATACTAATTTTTTTGTAATTTTTCTGATTTTTGTA-T
61 ATAAATAAACATACTAATTTTTTTGTAAATTTTCT-ATTTTTGTATT
* *
669716 TTTTCTGATTTTTTTAAATTCAAGTAGATTAATTTGCAAGATAAAAAT-ATTGAAATTAGATAAA
1 TTTTCTGATTTTTTTAAATTCAAATAGATTAATTTGCAAGATAAAAATAATTGAAATTAAATAAA
669780 TAAACATACTAATTTTTTTGTAAATTTTCTATTTTTGTATT
66 TAAACATACTAATTTTTTTGTAAATTTTCTATTTTTGTATT
*
669821 TTTTCTGATTTTTTTTAATTCAAATAGAT
1 TTTTCTGATTTTTTTAAATTCAAATAGAT
669850 ATTTTTAGAA
Statistics
Matches: 122, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
104 9 0.07
105 71 0.58
107 8 0.07
109 7 0.06
110 7 0.06
111 20 0.16
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (106 bp):
TTTTCTGATTTTTTTAAATTCAAATAGATTAATTTGCAAGATAAAAATAATTGAAATTAAATAAA
TAAACATACTAATTTTTTTGTAAATTTTCTATTTTTGTATT
Found at i:669816 original size:17 final size:18
Alignment explanation
Indices: 669794--669833 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
669784 CATACTAATT
669794 TTTTTGTAAATTTTCT-A
1 TTTTTGTAAATTTTCTGA
**
669811 TTTTTGTATTTTTTCTGA
1 TTTTTGTAAATTTTCTGA
669829 TTTTT
1 TTTTT
669834 TTTAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.72
Consensus pattern (18 bp):
TTTTTGTAAATTTTCTGA
Found at i:670003 original size:16 final size:17
Alignment explanation
Indices: 669968--670007 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
669958 GTTTCATCTC
**
669968 TAGAGATAGAGATACGT
1 TAGAGATAGAGATAAAT
669985 TAGA-ATAGAGATAAAT
1 TAGAGATAGAGATAAAT
670001 TAGAGAT
1 TAGAGAT
670008 GACCTAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.47, C:0.03, G:0.25, T:0.25
Consensus pattern (17 bp):
TAGAGATAGAGATAAAT
Found at i:672870 original size:21 final size:21
Alignment explanation
Indices: 672846--672888 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
672836 TTTGAAATAT
* *
672846 ATATAATATGTAATTTTTAAA
1 ATATAAAATATAATTTTTAAA
*
672867 ATATAAAATATAGTTTTTAAA
1 ATATAAAATATAATTTTTAAA
672888 A
1 A
672889 CATTTTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATAAAATATAATTTTTAAA
Found at i:672915 original size:37 final size:36
Alignment explanation
Indices: 672867--673083 Score: 229
Period size: 36 Copynumber: 6.1 Consensus size: 36
672857 AATTTTTAAA
*
672867 ATATAAAATATAGTTTTTAAAACATTTTGAAAAATAT
1 ATATAATATATAGTTTTTAAAACATTTTG-AAAATAT
*
672904 ATATAATATATAGTTTTTAAAATATTTTGAAAATAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAT
672940 ATATTAATATATAGTTTTT-AAACATTTTGAAAATAT
1 ATA-TAATATATAGTTTTTAAAACATTTTGAAAATAT
**
672976 ATAT-ATAATATAGTTTTTAAAACATTTAAAAAACT-T
1 ATATAAT-ATATAGTTTTTAAAACATTTTGAAAA-TAT
* * *
673012 A-AT-CTATATA-TTTTTGAAATCA-TCTG-AAAT-T
1 ATATAATATATAGTTTTT-AAAACATTTTGAAAATAT
*
673043 -TATAATATATAGTTTTAAAAAAGCATTTTGAAAATAT
1 ATATAATATATAGTTTT-TAAAA-CATTTTGAAAATAT
673080 ATAT
1 ATAT
673084 GATTTTTAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 27
0.79 0.07 0.14
Matches are distributed among these distances:
31 4 0.03
32 9 0.06
33 13 0.09
34 14 0.09
35 18 0.12
36 47 0.31
37 44 0.29
38 3 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATAT
Found at i:672967 original size:36 final size:37
Alignment explanation
Indices: 672874--673083 Score: 207
Period size: 37 Copynumber: 5.9 Consensus size: 37
672864 AAAATATAAA
672874 ATATAGTTTTTAAAACATTTTGAAAA-ATATATATAAT
1 ATATAGTTTTTAAAACATTTTGAAAATATATAT-TAAT
*
672911 ATATAGTTTTTAAAATATTTTGAAAATATATATTAAT
1 ATATAGTTTTTAAAACATTTTGAAAATATATATTAAT
672948 ATATAGTTTTT-AAACATTTTGAAAATATATA-T-AT
1 ATATAGTTTTTAAAACATTTTGAAAATATATATTAAT
*
672982 AATATAGTTTTTAAAACA-TTT-AAAA-A-A-CTTAATCT
1 -ATATAGTTTTTAAAACATTTTGAAAATATATATTAA--T
* *
673017 ATATA-TTTTTGAAATCA-TCTG-AAAT-T-TA-TAAT
1 ATATAGTTTTT-AAAACATTTTGAAAATATATATTAAT
*
673049 ATATAGTTTTAAAAAAGCATTTTGAAAATATATAT
1 ATATAGTTTT-TAAAA-CATTTTGAAAATATATAT
673084 GATTTTTAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 38
0.75 0.05 0.20
Matches are distributed among these distances:
32 8 0.06
33 14 0.10
34 26 0.18
35 19 0.13
36 28 0.19
37 41 0.28
38 8 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATAGTTTTTAAAACATTTTGAAAATATATATTAAT
Found at i:673114 original size:32 final size:31
Alignment explanation
Indices: 672874--673147 Score: 133
Period size: 30 Copynumber: 8.2 Consensus size: 31
672864 AAAATATAAA
*
672874 ATATAGTTTTTAAAACATTTTGAAAAATATATATAAT
1 ATATA-TTTTTAAAACATTTTG--AAA-A-CTAT-AT
* *
672911 ATATAGTTTTTAAAATATTTTGAAAATATATATT
1 ATATA-TTTTTAAAACATTTTGAAAA-CTATA-T
* *
672945 AATATATAGTTTTTAAACATTTTGAAAATATATATAT
1 -ATATAT--TTTTAAAACATTTTG-AAA-A-CTATAT
** *
672982 AATATAGTTTTTAAAACATTTAAAAAACTTAATCT
1 -ATATA-TTTTTAAAACATTTTGAAAAC-T-ATAT
* * **
673017 ATATATTTTTGAAATCA-TCTGAAATTTATAAT
1 ATATATTTTT-AAAACATTTTGAAAACTAT-AT
*
673049 ATATAGTTTTAAAAAAGCATTTTGAAAA-TATAT
1 ATATA-TTTT-TAAAA-CATTTTGAAAACTATAT
*
673082 AT-GATTTTTAAAACATTTTGAAAACTATAT
1 ATATATTTTTAAAACATTTTGAAAACTATAT
* * * * *
673112 ATATA-GTTGAAAACTTTTTAAAAATTATAT
1 ATATATTTTTAAAACATTTTGAAAACTATAT
673142 ATATAT
1 ATATAT
673148 AGTTTTCAAT
Statistics
Matches: 192, Mismatches: 27, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
29 11 0.06
30 36 0.19
31 7 0.04
32 8 0.04
33 21 0.11
34 25 0.13
35 20 0.10
36 25 0.13
37 31 0.16
38 8 0.04
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATATTTTTAAAACATTTTGAAAACTATAT
Found at i:673209 original size:17 final size:18
Alignment explanation
Indices: 673187--673223 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
673177 ATATATTATA
673187 TTATTTTA-TTATCTATT
1 TTATTTTATTTATCTATT
*
673204 TTATTTTATTTATTTATT
1 TTATTTTATTTATCTATT
673222 TT
1 TT
673224 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTATTTATCTATT
Found at i:673649 original size:12 final size:12
Alignment explanation
Indices: 673607--673649 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
673597 CCCCCCGATT
673607 ACCCGATA-CCG
1 ACCCGATACCCG
*
673618 CCCCGATTACCCG
1 ACCCGA-TACCCG
673631 -CCCGATACCCG
1 ACCCGATACCCG
673642 ACCCGATA
1 ACCCGATA
673650 AATATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 11 0.39
12 14 0.50
13 3 0.11
ACGTcount: A:0.23, C:0.49, G:0.16, T:0.12
Consensus pattern (12 bp):
ACCCGATACCCG
Found at i:673736 original size:25 final size:26
Alignment explanation
Indices: 673674--673740 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 26
673664 TTATTTATAT
673674 ATATATAATATTAATAATTTAATTTAA
1 ATATAT-ATATTAATAATTTAATTTAA
673701 ATAAAAAATATATATTAAT-ATTTAATTTAA
1 AT-----ATATATATTAATAATTTAATTTAA
673731 ATATATATAT
1 ATATATATAT
673741 CCCGGCCCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
25 8 0.23
27 2 0.06
30 13 0.37
31 8 0.23
32 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATATATTAATAATTTAATTTAA
Found at i:673773 original size:12 final size:12
Alignment explanation
Indices: 673758--673791 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
673748 CGATTCTCGG
673758 CCCAATACCCGA
1 CCCAATACCCGA
*
673770 CCCAATACCCGG
1 CCCAATACCCGA
673782 CCCAATACCC
1 CCCAATACCC
673792 TTTAAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.53, G:0.09, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:674125 original size:22 final size:20
Alignment explanation
Indices: 674079--674118 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
674069 ACGGGGAGCA
*
674079 ACACAAAACACAAATCGAAC
1 ACACAAAACACAAATCAAAC
674099 ACACAGAAACACAGAATCAA
1 ACACA-AAACACA-AATCAA
674119 GACCACAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.60, C:0.28, G:0.07, T:0.05
Consensus pattern (20 bp):
ACACAAAACACAAATCAAAC
Found at i:676351 original size:37 final size:37
Alignment explanation
Indices: 676309--676382 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
676299 ATATTTCAAC
676309 AAACATCTACCAAACTTTGAAAACCCA-TTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAA-CCATTTTTTCAAAG
*
676346 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAACCATTTTTTCAAAG
676383 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 3 0.09
37 32 0.91
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (37 bp):
AAACATCTACCAAACTTTGAAAACCATTTTTTCAAAG
Found at i:680930 original size:34 final size:34
Alignment explanation
Indices: 680832--680931 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
680822 ATATTTCAAC
* * *
680832 AAACATCTACCAAACTTTAAAAAACTATTTTTCAAAG
1 AAACATTTACC-AACTTT-GAAAACCA-TTTTCAAAG
* *
680869 AAACATTTACCAAATTGTG-AAATCATTTTCAAAG
1 AAACATTTACCAACTT-TGAAAACCATTTTCAAAG
680903 AAACATTTACCAACTTTGAAAACCATTTT
1 AAACATTTACCAACTTTGAAAACCATTTT
680932 TTCAAAGTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
33 2 0.04
34 33 0.61
35 4 0.07
36 4 0.07
37 11 0.20
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (34 bp):
AAACATTTACCAACTTTGAAAACCATTTTCAAAG
Found at i:687767 original size:24 final size:24
Alignment explanation
Indices: 687740--687796 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
687730 TTGATACTTG
** *
687740 AACAAAATAAAGTCACCATACATT
1 AACAAAATAAAACCACCAAACATT
*
687764 AACAAAATAAAACCACCAAACTTT
1 AACAAAATAAAACCACCAAACATT
687788 AACAAAATA
1 AACAAAATA
687797 TTACAAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.60, C:0.21, G:0.02, T:0.18
Consensus pattern (24 bp):
AACAAAATAAAACCACCAAACATT
Found at i:689779 original size:31 final size:31
Alignment explanation
Indices: 689741--689918 Score: 126
Period size: 31 Copynumber: 5.4 Consensus size: 31
689731 AAACTACCTA
689741 TTTGGTCACTTATATATTATCTAATTTATGT
1 TTTGGTCACTTATATATTATCTAATTTATGT
* ** *
689772 TTTGGTCAC-TAGATTATTATCTAGGGTAAACTATCT
1 TTTGGTCACTTATA-TATTATC-----TAATTTATGT
689808 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
** ** **
689840 TTTGGTCA-TTCGATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACTT--A-TA-TA-TTA-TCTAATTTATGT
689876 CTTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
689908 TTTGGTCACTT
1 TTTGGTCACTT
689919 TAGGGTAAAT
Statistics
Matches: 111, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
30 5 0.05
31 35 0.32
32 14 0.13
33 5 0.05
34 4 0.04
35 5 0.05
36 14 0.13
37 24 0.22
38 5 0.05
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:689823 original size:68 final size:68
Alignment explanation
Indices: 689723--690049 Score: 389
Period size: 68 Copynumber: 5.0 Consensus size: 68
689713 TTAGGATTTT
*
689723 TTTAGAGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
689788 TTA
66 TTA
* * * *
689791 TCTAGGGTAAACTATCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCATTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
689856 TTA
66 TTA
*
689859 TTTAGGGTAAACTACCTCTTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCAC-------
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
689917 ---
66 TTA
* * ** ** * *
689917 TTTAGGGTAAATTGCCTATTTGGTCACTTATATATTATCTAA--TA--TAATCAT-A-TATATTT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
689976 TTA
66 TTA
* * *
689979 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATATAATTTATGTTTTGGTCAATCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
690044 TTA
66 TTA
690047 TTT
1 TTT
690050 TTTTCAAAAT
Statistics
Matches: 217, Mismatches: 26, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
53 1 0.00
54 3 0.01
56 2 0.01
58 39 0.18
62 39 0.18
64 2 0.01
66 3 0.01
67 1 0.00
68 127 0.59
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTAGATTA
TTA
Found at i:689827 original size:37 final size:34
Alignment explanation
Indices: 689728--689899 Score: 101
Period size: 37 Copynumber: 5.0 Consensus size: 34
689718 ATTTTTTTAG
*
689728 AGTAAACTACCTATTTGGTCACTTATATATTATC-
1 AGTAAACTATCT-TTTGGTCACTTATATATTATCT
** * *
689762 --TAATTTATGTTTTGGTCAC-TAGATTATTATCT
1 AGTAAACTATCTTTTGGTCACTTATA-TATTATCT
689794 AGGGTAAACTATCTATTTGGTCACTTATATATTATC-
1 A--GTAAACTATCT-TTTGGTCACTTATATATTATCT
** * *
689830 --TAATTTATGTTTTGGTCA-TTCGAT-TATTATTT
1 AGTAAACTATCTTTTGGTCACTT--ATATATTATCT
*
689862 AGGGTAAACTACCTCTTTGGTCACTTATATATTATCT
1 A--GTAAACTATCT-TTTGGTCACTTATATATTATCT
689899 A
1 A
689900 ATTTATGTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 33
0.67 0.12 0.22
Matches are distributed among these distances:
30 5 0.05
31 30 0.29
32 15 0.15
36 15 0.15
37 32 0.31
38 5 0.05
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (34 bp):
AGTAAACTATCTTTTGGTCACTTATATATTATCT
Found at i:689949 original size:58 final size:57
Alignment explanation
Indices: 689858--690035 Score: 223
Period size: 58 Copynumber: 3.0 Consensus size: 57
689848 TTCGATTATT
*
689858 ATTTAGGGTAAACTACCTCTTTGGTCACTTATATATTATCTAATTTATGTTTTGGTC
1 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTC
* * * * *
689915 ACTTTAGGGTAAATTGCCTATTTGGTCACTTATATATTATCTAATATAATCATATATATT-TTT
1 A-TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-T--T-ATGT-T-TTGGTC
*
689978 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATATAATTTATGTTTTGGTC
1 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTC
690035 A
1 A
690036 ATCGATTATT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
56 2 0.02
57 4 0.04
58 43 0.43
59 2 0.02
61 2 0.02
62 43 0.43
63 3 0.03
64 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (57 bp):
ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTC
Found at i:690477 original size:31 final size:30
Alignment explanation
Indices: 690403--690477 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
690393 ATTTGATACG
*
690403 TATAT-TTTTACAAAATATCTAATGTGCTA
1 TATATATTTTATAAAATATCTAATGTGCTA
* * *
690432 TATATAATTT-TAAAATATCTATTGTGTTA
1 TATATATTTTATAAAATATCTAATGTGCTA
*
690461 TTTATATTTTAATAAAA
1 TATATATTTT-ATAAAA
690478 AAATTGTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 29 0.78
30 3 0.08
31 5 0.14
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (30 bp):
TATATATTTTATAAAATATCTAATGTGCTA
Found at i:690603 original size:31 final size:30
Alignment explanation
Indices: 690533--690614 Score: 112
Period size: 29 Copynumber: 2.7 Consensus size: 30
690523 TTATGTTTTT
* *
690533 TTATTAAAATGTCTAATATAATATTTATAC
1 TTATTAAAATATCTAATATAATATCTATAC
*
690563 TT-TTAAAATATCCAATATAATATCTATAC
1 TTATTAAAATATCTAATATAATATCTATAC
*
690592 TTCATTAAAATATTTAATATAAT
1 TT-ATTAAAATATCTAATATAAT
690615 GCATGGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.58
30 2 0.04
31 17 0.38
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (30 bp):
TTATTAAAATATCTAATATAATATCTATAC
Found at i:690852 original size:29 final size:30
Alignment explanation
Indices: 690820--690890 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
690810 CGCATAAACC
690820 TTTTAAAAGTACAAGTATCACATTAAATAT
1 TTTTAAAAGTACAAGTATCACATTAAATAT
* * *
690850 TTTGTAAAAATGCAGGTATCACATTAAATA-
1 TTT-TAAAAGTACAAGTATCACATTAAATAT
*
690880 TTCTAAAAGTA
1 TTTTAAAAGTA
690891 TAGATACCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 6 0.18
30 5 0.15
31 23 0.68
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTTAAAAGTACAAGTATCACATTAAATAT
Found at i:699688 original size:59 final size:60
Alignment explanation
Indices: 699616--699739 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 60
699606 TTATACCATA
* *
699616 ATTATAAGGTATTATTTTGTTGAG-TTCT-TAATTTTTAAAAATTATAAAATGAT-ATTATG
1 ATTATAAGATATTATTTTGTTGAGTTTCTCT-ATTATTAAAAATTATAAAATGATCATTA-G
**
699675 ATTATAAGATATTATTTTGTTGAGTTTCTCTATTATTAAACGTTATAAAATGATCATTAG
1 ATTATAAGATATTATTTTGTTGAGTTTCTCTATTATTAAAAATTATAAAATGATCATTAG
699735 ATTAT
1 ATTAT
699740 TTATATGTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
59 23 0.40
60 30 0.52
61 5 0.09
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.48
Consensus pattern (60 bp):
ATTATAAGATATTATTTTGTTGAGTTTCTCTATTATTAAAAATTATAAAATGATCATTAG
Found at i:701086 original size:20 final size:19
Alignment explanation
Indices: 701061--701127 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
701051 TTTTCCTAAT
701061 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAAT-CGTAAA
* * *
701081 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA--TCGTAAA
701102 TCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATC-GTAAA
701122 TCGCAA
1 TCGCAA
701128 CGAGATTCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 21 0.55
21 15 0.39
22 1 0.03
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
TCGCAATGCGAATCGTAAA
Found at i:701104 original size:21 final size:20
Alignment explanation
Indices: 701078--701129 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
701068 GCGAATACGT
*
701078 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATCT-GA
* *
701099 AAATCGCAATGCGAATCTGT
1 AAATCGCAACGCGAATCTGA
701119 AAATCGCAACG
1 AAATCGCAACG
701130 AGATTCTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCTGA
Found at i:701137 original size:20 final size:20
Alignment explanation
Indices: 701076--701137 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
701066 ATGCGAATAC
701076 GTAAATCGCAACGCGAATT-T
1 GTAAATCGCAACGCG-ATTCT
* * *
701096 GGAAAATCGCAATGCGAATCT
1 -GTAAATCGCAACGCGATTCT
*
701117 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGCGATTCT
701137 G
1 G
701138 ACTATCGCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (20 bp):
GTAAATCGCAACGCGATTCT
Found at i:702016 original size:24 final size:24
Alignment explanation
Indices: 701989--702042 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
701979 GTATTCGAAA
701989 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
702013 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
702037 TTTGAT
1 TTTGAT
702043 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.