Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold483
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: 459596
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:177343 original size:22 final size:24
Alignment explanation
Indices: 177318--177368 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
177308 ATAAAACATA
177318 AATTATAT-TA-TTATTATAATAT
1 AATTATATGTATTTATTATAATAT
*
177340 AATT-T-TGTATTTATTATTATAT
1 AATTATATGTATTTATTATAATAT
177362 -ATTATAT
1 AATTATAT
177369 ATAAAGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 1 0.04
21 6 0.25
22 16 0.67
23 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AATTATATGTATTTATTATAATAT
Found at i:177844 original size:19 final size:20
Alignment explanation
Indices: 177820--177859 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
177810 AGGTCAAAAC
177820 CCTT-AAATGTATCGATACA
1 CCTTAAAATGTATCGATACA
177839 CCTTAAAATGTATCGATACA
1 CCTTAAAATGTATCGATACA
177859 C
1 C
177860 AATGCACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (20 bp):
CCTTAAAATGTATCGATACA
Found at i:177905 original size:20 final size:21
Alignment explanation
Indices: 177880--177932 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
177870 ATTGATACAT
*
177880 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
177900 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
177921 TGTATCGATACA
1 TGTATCGATACA
177933 GGTCATTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:178010 original size:13 final size:13
Alignment explanation
Indices: 177992--178017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177982 TGCACACAAG
177992 ATGTATCGATACA
1 ATGTATCGATACA
178005 ATGTATCGATACA
1 ATGTATCGATACA
178018 TCCCAAAATG
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:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:178033 original size:33 final size:32
Alignment explanation
Indices: 177974--178037 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
177964 CTTAACTGTT
* *
177974 TGTATCGATGCACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
178006 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
178038 TTGGCTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:183913 original size:13 final size:13
Alignment explanation
Indices: 183895--183919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183885 CAGTATTTTC
183895 TGTATCGATACAT
1 TGTATCGATACAT
183908 TGTATCGATACA
1 TGTATCGATACA
183920 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:184385 original size:20 final size:22
Alignment explanation
Indices: 184360--184404 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
184350 GCAGCACTCA
184360 CCAGGTCACAACC-GGC-ACCC
1 CCAGGTCACAACCGGGCAACCC
*
184380 CCAGGTCGCAACCGGGCAACCC
1 CCAGGTCACAACCGGGCAACCC
184402 CCA
1 CCA
184405 CACTGGTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 3 0.14
22 7 0.32
ACGTcount: A:0.24, C:0.49, G:0.22, T:0.04
Consensus pattern (22 bp):
CCAGGTCACAACCGGGCAACCC
Found at i:186355 original size:19 final size:20
Alignment explanation
Indices: 186331--186369 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
186321 AGGTCAAAAC
186331 CCTT-AAATGTATCGATACA
1 CCTTAAAATGTATCGATACA
186350 CCTTAAAATGTATCGATACA
1 CCTTAAAATGTATCGATACA
186370 TAATACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
CCTTAAAATGTATCGATACA
Found at i:186395 original size:13 final size:13
Alignment explanation
Indices: 186379--186403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186369 ATAATACACA
186379 GTATCGATACATT
1 GTATCGATACATT
186392 GTATCGATACAT
1 GTATCGATACAT
186404 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:186416 original size:20 final size:21
Alignment explanation
Indices: 186391--186443 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
186381 ATCGATACAT
*
186391 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
186411 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
186432 TGTATCGATACA
1 TGTATCGATACA
186444 GGTCATTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:186528 original size:20 final size:20
Alignment explanation
Indices: 186485--186536 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
186475 CTTAACTATT
*
186485 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
186504 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
186524 TGTATCGATACAT
1 TGTATCGATACAT
186537 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:187889 original size:112 final size:114
Alignment explanation
Indices: 187771--187977 Score: 321
Period size: 115 Copynumber: 1.8 Consensus size: 114
187761 TCGAAATCCA
*
187771 TTTTCCTTTGTCTAGGTCTTTTATTTCATTA-TTTTTT-ATATTTTCAAAAAAATAAA-AAATAA
1 TTTTCCTTTGTCTAGGACTTTTATTTCATTATTTTTTTGAT-TTTTCAAAAAAATAAAGAAATAA
*
187833 TAAAGTAAAATAAAAATTAAGAAAATGAATCGAAAAATAAGAAAATTTTC
65 CAAAGTAAAATAAAAATTAAGAAAATGAATCGAAAAATAAGAAAATTTTC
* * *
187883 TTTTCCTTTTTCTAGGACTTTTATTTTATTATTTTTTTGGATTTTTGAAAAAAATAAAGAAATAA
1 TTTTCCTTTGTCTAGGACTTTTATTTCATTATTTTTTT-GATTTTTCAAAAAAATAAAGAAATAA
*
187948 CAAAGTAAAATAAAACTTAAGAAAATGAAT
65 CAAAGTAAAATAAAAATTAAGAAAATGAAT
187978 AAAAAAAAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 28 0.33
113 6 0.07
114 15 0.18
115 36 0.42
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (114 bp):
TTTTCCTTTGTCTAGGACTTTTATTTCATTATTTTTTTGATTTTTCAAAAAAATAAAGAAATAAC
AAAGTAAAATAAAAATTAAGAAAATGAATCGAAAAATAAGAAAATTTTC
Found at i:187984 original size:115 final size:111
Alignment explanation
Indices: 187771--187988 Score: 312
Period size: 112 Copynumber: 1.9 Consensus size: 111
187761 TCGAAATCCA
* *
187771 TTTTCCTTTGTCTAGGTCTTTTATTTCATTATTTTTTATATTTTCAAAAAAATAAAAAATAATAA
1 TTTTCCTTTGTCTAGGACTTTTATTTCATTATTTTTTATATTTTCAAAAAAATAAAAAATAACAA
* *
187836 AGTAAAATAAAAATTAAGAAAATGAATCGAAAAATAAGAAAATTTTC
66 AGTAAAATAAAAATTAAGAAAATGAAT-AAAAAAAAAGAAAATTTTC
* * *
187883 TTTTCCTTTTTCTAGGACTTTTATTTTATTATTTTTT-TGGATTTTTGAAAAAAATAAAGAAATA
1 TTTTCCTTTGTCTAGGACTTTTATTTCATTATTTTTTAT--A-TTTTCAAAAAAATAAA-AAATA
*
187947 ACAAAGTAAAATAAAACTTAAGAAAATGAATAAAAAAAAAGA
62 ACAAAGTAAAATAAAAATTAAGAAAATGAATAAAAAAAAAGA
187989 GAGGAGAGGA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
111 1 0.01
112 34 0.36
113 1 0.01
114 24 0.26
115 34 0.36
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (111 bp):
TTTTCCTTTGTCTAGGACTTTTATTTCATTATTTTTTATATTTTCAAAAAAATAAAAAATAACAA
AGTAAAATAAAAATTAAGAAAATGAATAAAAAAAAAGAAAATTTTC
Found at i:191421 original size:3 final size:3
Alignment explanation
Indices: 191413--191440 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
191403 TTTATTTGTA
191413 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
191441 CATTTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:192449 original size:19 final size:19
Alignment explanation
Indices: 192425--192461 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
192415 TCTATTTTAT
192425 TTCCACTTTGAAACTAAGA
1 TTCCACTTTGAAACTAAGA
*
192444 TTCCACTTTTAAACTAAG
1 TTCCACTTTGAAACTAAG
192462 GCGTAGTTTT
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:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (19 bp):
TTCCACTTTGAAACTAAGA
Found at i:192935 original size:17 final size:18
Alignment explanation
Indices: 192913--192961 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
192903 TTTTTTTGAT
*
192913 ATAAAATTAAAATAA-TA
1 ATAAAATTAAAAAAATTA
192930 ATAAAA-TAAAAAAATTA
1 ATAAAATTAAAAAAATTA
*
192947 AAAAAATTAAAAAAA
1 ATAAAATTAAAAAAA
192962 AATCGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 13 0.46
18 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAATTAAAAAAATTA
Found at i:192962 original size:10 final size:9
Alignment explanation
Indices: 192915--192961 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
192905 TTTTTGATAT
192915 AAAATTAAA
1 AAAATTAAA
* *
192924 ATAA-TAAT
1 AAAATTAAA
192932 AAAA-TAAA
1 AAAATTAAA
192940 AAAATTAAA
1 AAAATTAAA
192949 AAAATTAAA
1 AAAATTAAA
192958 AAAA
1 AAAA
192962 AATCGAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 13 0.39
9 20 0.61
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:200755 original size:3 final size:3
Alignment explanation
Indices: 200747--200787 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
200737 TGGAAACTAC
200747 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
200788 GGTTTATAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:203626 original size:15 final size:15
Alignment explanation
Indices: 203606--203638 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
203596 TCAACGAGCT
203606 ACTTCATCATCCCAA
1 ACTTCATCATCCCAA
*
203621 ACTTCATTATCCCAA
1 ACTTCATCATCCCAA
203636 ACT
1 ACT
203639 ACTCCGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (15 bp):
ACTTCATCATCCCAA
Found at i:210879 original size:31 final size:30
Alignment explanation
Indices: 210811--210916 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
210801 TGTAACCTTC
* *
210811 TCAAAGTCCACGACTTAGTGGCATCTTTTT
1 TCAAAGTCCACGACTCAATGGCATCTTTTT
210841 TCAAAGTCCACGACTCAATGGCATCCTTTTT
1 TCAAAGTCCACGACTCAATGGCAT-CTTTTT
** * * *
210872 TTTAAGTCCATGACTCAATGACATCTCTTT
1 TCAAAGTCCACGACTCAATGGCATCTTTTT
210902 TCAAAGTCCACGACT
1 TCAAAGTCCACGACT
210917 TACTGGCACC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 39 0.60
31 26 0.40
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (30 bp):
TCAAAGTCCACGACTCAATGGCATCTTTTT
Found at i:210903 original size:61 final size:60
Alignment explanation
Indices: 210814--210929 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
210804 AACCTTCTCA
* * * *
210814 AAGTCCACGACTTAGTGGCATCTTTTTTCAAAGTCCACGACTCAATGGCATCCTTTTTTTT
1 AAGTCCACGACTCAATGACATCTCTTTTCAAAGTCCACGACTCAATGGCA-CCTTTTTTTT
* * *
210875 AAGTCCATGACTCAATGACATCTCTTTTCAAAGTCCACGACTTACTGGCACCTTT
1 AAGTCCACGACTCAATGACATCTCTTTTCAAAGTCCACGACTCAATGGCACCTTT
210930 ATTAAAATCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 5 0.10
61 43 0.90
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (60 bp):
AAGTCCACGACTCAATGACATCTCTTTTCAAAGTCCACGACTCAATGGCACCTTTTTTTT
Found at i:210999 original size:33 final size:33
Alignment explanation
Indices: 210956--211069 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
210946 TCGTGACACC
210956 TTTTCTTTTTAAAGTCCACAACTTCATGGCATAT
1 TTTTC-TTTTAAAGTCCACAACTTCATGGCATAT
* *
210990 TTTTCTTTTAAAGTCTACAA-TTCCATGGCACAT
1 TTTTCTTTTAAAGTCCACAACTT-CATGGCATAT
* *
211023 TTTTCTTTTGAAGTCCACAACTCCATGGCACT-T
1 TTTTCTTTTAAAGTCCACAACTTCATGGCA-TAT
*
211056 TTTTATTTTAAAGT
1 TTTTCTTTTAAAGT
211070 TTATAACTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.03
33 61 0.88
34 6 0.09
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (33 bp):
TTTTCTTTTAAAGTCCACAACTTCATGGCATAT
Found at i:211037 original size:66 final size:67
Alignment explanation
Indices: 210956--211092 Score: 179
Period size: 66 Copynumber: 2.1 Consensus size: 67
210946 TCGTGACACC
* * *
210956 TTTTCTTTTTAAAGTCCACAACTTCATGGCA-TATTTTTCTTTTAAAGTCTACAATTCCATGGCA
1 TTTTCTTTTTAAAGTCCACAACTCCATGGCACT-TTTTTATTTTAAAGTCTACAACTCCATGGCA
211020 CAT
65 CAT
* * * *
211023 TTTTC-TTTTGAAGTCCACAACTCCATGGCACTTTTTTATTTTAAAGTTTATAACTCCGTGGCAC
1 TTTTCTTTTTAAAGTCCACAACTCCATGGCACTTTTTTATTTTAAAGTCTACAACTCCATGGCAC
*
211087 CT
66 AT
211089 TTTT
1 TTTT
211093 AAGTCCATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
66 55 0.90
67 6 0.10
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (67 bp):
TTTTCTTTTTAAAGTCCACAACTCCATGGCACTTTTTTATTTTAAAGTCTACAACTCCATGGCAC
AT
Found at i:211078 original size:33 final size:33
Alignment explanation
Indices: 210931--211093 Score: 141
Period size: 33 Copynumber: 4.9 Consensus size: 33
210921 GGCACCTTTA
* * * * *
210931 TTAAAATCTACAACTTCGTGACACCTTTTCT-TT
1 TTAAAGTCTACAACTCCATGGCA-CTTTTTTATT
* * *
210964 TTAAAGTCCACAACTTCATGGCA-TATTTTTCTT
1 TTAAAGTCTACAACTCCATGGCACT-TTTTTATT
* * *
210997 TTAAAGTCTACAATTCCATGGCACATTTTTCTT
1 TTAAAGTCTACAACTCCATGGCACTTTTTTATT
* *
211030 TTGAAGTCCACAACTCCATGGCACTTTTTTATT
1 TTAAAGTCTACAACTCCATGGCACTTTTTTATT
* * * *
211063 TTAAAGTTTATAACTCCGTGGCACCTTTTTA
1 TTAAAGTCTACAACTCCATGGCACTTTTTTA
211094 AGTCCATAAC
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.01
32 4 0.04
33 102 0.95
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (33 bp):
TTAAAGTCTACAACTCCATGGCACTTTTTTATT
Found at i:211196 original size:33 final size:33
Alignment explanation
Indices: 211158--211243 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
211148 TTTAAGTCCG
* *
211158 CAACTCCTTGGCACTTTTTTTTTTAAAAATCCA
1 CAACTCCTTGGCACCTTTTTCTTTAAAAATCCA
* *
211191 CAACT-CTATGGCACCTTTTTCTTTCAAAGTCCA
1 CAACTCCT-TGGCACCTTTTTCTTTAAAAATCCA
* * *
211224 TAACTCCGTGGCACCCTTTT
1 CAACTCCTTGGCACCTTTTT
211244 AAGTCCACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 41 0.93
34 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.38
Consensus pattern (33 bp):
CAACTCCTTGGCACCTTTTTCTTTAAAAATCCA
Found at i:211250 original size:27 final size:27
Alignment explanation
Indices: 211217--211328 Score: 100
Period size: 27 Copynumber: 4.0 Consensus size: 27
211207 TTTTCTTTCA
* *
211217 AAGTCCATAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCATGGCACCCTTTT
* *
211244 AAGTCCACAACTTCATGACACCTTTTTCTTTT
1 AAGTCCACAACTCCATGGCACC-----CTTTT
* * *
211276 AAGTCCATAACTCCGTGGTACCCTTTT
1 AAGTCCACAACTCCATGGCACCCTTTT
*
211303 AAGTCCACAATTCCATGGCA-CCTTTT
1 AAGTCCACAACTCCATGGCACCCTTTT
211329 CCTTCAAAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
26 6 0.09
27 39 0.58
32 22 0.33
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (27 bp):
AAGTCCACAACTCCATGGCACCCTTTT
Found at i:211299 original size:59 final size:60
Alignment explanation
Indices: 211187--211336 Score: 218
Period size: 59 Copynumber: 2.5 Consensus size: 60
211177 TTTTTAAAAA
211187 TCCACAAC-TCTATGGCACCTTTTTCTTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAG
1 TCCACAACTTC-ATGGCACCTTTTTCTTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAG
* * *
211247 TCCACAACTTCATGACACCTTTTTCTTT-TAAGTCCATAACTCCGTGGTACCCTTTTAAG
1 TCCACAACTTCATGGCACCTTTTTCTTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAG
*
211306 TCCACAA-TTCCATGGCACC-TTTTCCTTCAAA
1 TCCACAACTT-CATGGCACCTTTTTCTTTCAAA
211337 ATCTACAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
58 9 0.11
59 46 0.57
60 24 0.30
61 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.35
Consensus pattern (60 bp):
TCCACAACTTCATGGCACCTTTTTCTTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAG
Found at i:211338 original size:151 final size:151
Alignment explanation
Indices: 210994--211346 Score: 404
Period size: 151 Copynumber: 2.3 Consensus size: 151
210984 GCATATTTTT
* ** * *
210994 CTTTTAAAGTCTACAATTCCATGGCACATTTTTCTTTTGAAGTCCACAACTCCATGGCACTTTTT
1 CTTTT-AAGTCCACAATTCCATGGCACATTTTTCTTTAAAAATCCACAACTCCATGGCACCTTTT
* ** * * * *
211059 TATTTTAAAGTTTATAACTCCGTGGCACCTTTTTAAGTCCATAACTCCCTGGCACCTTTTTTTTG
65 TATTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGACACCTTTTTTTTG
** *
211124 AAGCCTACAACTTTGTGGTGCC
130 AAGCCTACAACTCCGTGGTACC
* * * * * *
211146 CTTTTAAGTCCGCAACTCCTTGGCACTTTTTTTTTTAAAAATCCACAACTCTATGGCACCTTTTT
1 CTTTTAAGTCCACAATTCCATGGCACATTTTTCTTTAAAAATCCACAACTCCATGGCACCTTTTT
* * *
211211 CTTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTTCATGACACCTTTTTCTTTT
66 ATTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGACACCTTTTT-TTTG
*
211276 AAGTCC-ATAACTCCGTGGTACC
130 AAG-CCTACAACTCCGTGGTACC
* * * *
211298 CTTTTAAGTCCACAATTCCATGGCAC-CTTTTCCTTCAAAATCTACAACT
1 CTTTTAAGTCCACAATTCCATGGCACATTTTTCTTTAAAAATCCACAACT
211347 TGGTGGCACT
Statistics
Matches: 166, Mismatches: 33, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
151 118 0.71
152 46 0.28
153 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (151 bp):
CTTTTAAGTCCACAATTCCATGGCACATTTTTCTTTAAAAATCCACAACTCCATGGCACCTTTTT
ATTTCAAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGACACCTTTTTTTTGA
AGCCTACAACTCCGTGGTACC
Found at i:211391 original size:31 final size:31
Alignment explanation
Indices: 211346--211637 Score: 277
Period size: 31 Copynumber: 9.3 Consensus size: 31
211336 AATCTACAAC
*
211346 TTGGTGGC-A-CTTT-TAAAGTCCACATAAG
1 TTGGTGGCAACCTTTCTAAAGCCCACATAAG
* * *
211374 TTGGTAGCAACCTTTTTAAAGTCCACATAAG
1 TTGGTGGCAACCTTTCTAAAGCCCACATAAG
*
211405 TTGGTGGCAACCCTTCTCTAAAGCTCACATAAG
1 TTGGTGGCAA-CCTT-TCTAAAGCCCACATAAG
* * * *
211438 TCGATGGCAACCCTTCTAAAACCCACATAAG
1 TTGGTGGCAACCTTTCTAAAGCCCACATAAG
* * *
211469 TAGATGGTAACCTTTCTCCAAAGCCCACATAAG
1 TTGGTGGCAACCTTTCT--AAAGCCCACATAAG
*
211502 TTGATGGCAACCTTTCTAAAGCCCACATAAG
1 TTGGTGGCAACCTTTCTAAAGCCCACATAAG
** *
211533 TCAGTGGCAACCATTTCTAAAGCCCACACAAG
1 TTGGTGGCAACC-TTTCTAAAGCCCACATAAG
** * *
211565 TCAGTGGCAACCCTCTT-AAAAGCTCACATAAG
1 TTGGTGGCAA-CCT-TTCTAAAGCCCACATAAG
* * *
211597 TTAGTGGCAACCTTCTCAAAAGCCCACACAAG
1 TTGGTGGCAACCTT-TCTAAAGCCCACATAAG
211629 TTGGTGGCA
1 TTGGTGGCA
211638 TTTCCTTCTA
Statistics
Matches: 225, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.03
29 1 0.00
30 5 0.02
31 80 0.36
32 78 0.35
33 54 0.24
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (31 bp):
TTGGTGGCAACCTTTCTAAAGCCCACATAAG
Found at i:211434 original size:64 final size:64
Alignment explanation
Indices: 211359--211637 Score: 296
Period size: 64 Copynumber: 4.4 Consensus size: 64
211349 GTGGCACTTT
* * * * *
211359 TAAAGTCCACATAAGTTGGTAGCAACCTTTTTAAAGTCCACATAAGTTGGTGGCAACCCTTCTC
1 TAAAGCCCACATAAGTTGGTGGCAACCTTTCTAAAGCCCACATAAGTTAGTGGCAACCCTTCTC
* * * * * * *
211423 TAAAGCTCACATAAGTCGATGGCAACCCTTCTAAAACCCACATAAG-TAGATGGTAACCTTTCTC
1 TAAAGCCCACATAAGTTGGTGGCAACCTTTCTAAAGCCCACATAAGTTAG-TGGCAACCCTTCTC
* * * *
211487 CAAAGCCCACATAAGTTGATGGCAACCTTTCTAAAGCCCACATAAGTCAGTGGCAACCATT-TC
1 TAAAGCCCACATAAGTTGGTGGCAACCTTTCTAAAGCCCACATAAGTTAGTGGCAACCCTTCTC
* ** * *
211550 TAAAGCCCACACAAGTCAGTGGCAACCCTCTT-AAAAGCTCACATAAGTTAGTGGCAA-CCTTCT
1 TAAAGCCCACATAAGTTGGTGGCAA-CCT-TTCTAAAGCCCACATAAGTTAGTGGCAACCCTTCT
211613 C
64 C
* *
211614 AAAAGCCCACACAAGTTGGTGGCA
1 TAAAGCCCACATAAGTTGGTGGCA
211638 TTTCCTTCTA
Statistics
Matches: 178, Mismatches: 32, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
63 27 0.15
64 147 0.83
65 4 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (64 bp):
TAAAGCCCACATAAGTTGGTGGCAACCTTTCTAAAGCCCACATAAGTTAGTGGCAACCCTTCTC
Found at i:211465 original size:95 final size:94
Alignment explanation
Indices: 211365--211629 Score: 286
Period size: 95 Copynumber: 2.8 Consensus size: 94
211355 CTTTTAAAGT
* * * *
211365 CCACATAAGTTGGTAGCAACCTTTTTAAAGTCCACATAAGTTGGTGGCAACCCTTCTCTAAAGCT
1 CCACATAAGTAGGTGGCAACCTTTTAAAAG-CCACATAAGTTGGTGGCAA-CCTTCTCTAAAGCC
211430 CACATAAGTC-GATGGCAACC-CTTCTAAAAC
64 CACATAAGTCAG-TGGCAACCACTTCTAAAAC
* * * *
211460 CCACATAAGTAGATGGTAACCTTTCTCCAAAGCCCACATAAGTTGATGGCAACCTT-TCTAAAGC
1 CCACATAAGTAGGTGGCAACCTTT-T-AAAAG-CCACATAAGTTGGTGGCAACCTTCTCTAAAGC
* *
211524 CCACATAAGTCAGTGGCAACCATTTCTAAAGC
63 CCACATAAGTCAGTGGCAACCACTTCTAAAAC
* * * *
211556 CCACACAAGTCA-GTGGCAACCCTCTTAAAAGCTCACATAAGTTAGTGGCAACCTTCTCAAAAGC
1 CCACATAAGT-AGGTGGCAA-CCTTTTAAAAGC-CACATAAGTTGGTGGCAACCTTCTCTAAAGC
*
211620 CCACACAAGT
63 CCACATAAGT
211630 TGGTGGCATT
Statistics
Matches: 143, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
94 1 0.01
95 70 0.49
96 45 0.31
97 27 0.19
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (94 bp):
CCACATAAGTAGGTGGCAACCTTTTAAAAGCCACATAAGTTGGTGGCAACCTTCTCTAAAGCCCA
CATAAGTCAGTGGCAACCACTTCTAAAAC
Found at i:211630 original size:32 final size:32
Alignment explanation
Indices: 211359--211637 Score: 259
Period size: 32 Copynumber: 8.8 Consensus size: 32
211349 GTGGCACTTT
* * * *
211359 TAAAGTCCACATAAGTTGGTAGCAACCTT-TT
1 TAAAGCCCACATAAGTTAGTGGCAACCTTCTC
* *
211390 TAAAGTCCACATAAGTTGGTGGCAACCCTTCTC
1 TAAAGCCCACATAAGTTAGTGGCAA-CCTTCTC
* * *
211423 TAAAGCTCACATAAG-TCGATGGCAACCCT-TC
1 TAAAGCCCACATAAGTTAG-TGGCAACCTTCTC
* *
211454 TAAAACCCACATAAG-TAGATGGTAACCTTTCTC
1 TAAAGCCCACATAAGTTAG-TGGCAACC-TTCTC
*
211487 CAAAGCCCACATAAGTT-GATGGCAACCTT-TC
1 TAAAGCCCACATAAGTTAG-TGGCAACCTTCTC
*
211518 TAAAGCCCACATAAGTCAGTGGCAACCATT-TC
1 TAAAGCCCACATAAGTTAGTGGCAACC-TTCTC
* * *
211550 TAAAGCCCACACAAGTCAGTGGCAACCCTCT-
1 TAAAGCCCACATAAGTTAGTGGCAACCTTCTC
*
211581 TAAAAGCTCACATAAGTTAGTGGCAACCTTCTC
1 T-AAAGCCCACATAAGTTAGTGGCAACCTTCTC
* * *
211614 AAAAGCCCACACAAGTTGGTGGCA
1 TAAAGCCCACATAAGTTAGTGGCA
211638 TTTCCTTCTA
Statistics
Matches: 211, Mismatches: 26, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
31 76 0.36
32 90 0.43
33 44 0.21
34 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (32 bp):
TAAAGCCCACATAAGTTAGTGGCAACCTTCTC
Found at i:211831 original size:22 final size:22
Alignment explanation
Indices: 211803--211847 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
211793 TGGCGTCTTT
211803 TCATCTTTAAGTCCAATATCGC
1 TCATCTTTAAGTCCAATATCGC
211825 TCATCTTTAAGTCCAATATCGC
1 TCATCTTTAAGTCCAATATCGC
211847 T
1 T
211848 GGCCTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAGTCCAATATCGC
Found at i:211844 original size:73 final size:75
Alignment explanation
Indices: 211757--211898 Score: 207
Period size: 73 Copynumber: 1.9 Consensus size: 75
211747 TTTTTTCTTT
* * * *
211757 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCGTCTTT-TCA-TCTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAACAGATTGGCATCTTTGTCATTCTTTAAGTCCAAT
211820 ATCGCTCATC
66 ATCGCTCATC
* *
211830 TTTAAGTCCAATATCGCTGGCCTTGAATCAACAGATTGGCATCTTTGTCATTTTTTTTAGTCCAA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAACAGATTGGCATCTTTGTCA-TTCTTTAAGTCCAA
211895 TATC
65 TATC
211899 ATTGGCCTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 42 0.70
74 3 0.05
76 15 0.25
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (75 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAACAGATTGGCATCTTTGTCATTCTTTAAGTCCAAT
ATCGCTCATC
Found at i:212019 original size:52 final size:52
Alignment explanation
Indices: 211957--212150 Score: 140
Period size: 52 Copynumber: 3.6 Consensus size: 52
211947 AAGTCCAATG
*
211957 TCGCTGGCCTTGAATCAGCACATTGGCACTTTTGTTATCTTTAAGCCTAATA
1 TCGCTGGCCTTGAATCAGCACATTAGCACTTTTGTTATCTTTAAGCCTAATA
* * * * *
212009 TCGCTGGCCTTGAATTAGCATTTTGACACCTTTATCA-TTCTTCTCATCTTTAAGTCC-AATG
1 TCGCTGGCCTTGAA-T--CA----G-CA-CATTAGCACTT-TTGTTATCTTTAAG-CCTAATA
* * * * * *
212070 TCGTTGGCTTTGAATCATCACATTAGCACCTTTGTCATGTTTAAGCCTAATA
1 TCGCTGGCCTTGAATCAGCACATTAGCACTTTTGTTATCTTTAAGCCTAATA
* * *
212122 TCGTTGGCCTTGAATTAGCATATTAGCAC
1 TCGCTGGCCTTGAATCAGCACATTAGCAC
212151 CTTTATCATT
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
51 2 0.02
52 60 0.55
53 4 0.04
55 2 0.02
58 2 0.02
59 1 0.01
60 5 0.05
61 32 0.29
62 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (52 bp):
TCGCTGGCCTTGAATCAGCACATTAGCACTTTTGTTATCTTTAAGCCTAATA
Found at i:212100 original size:61 final size:61
Alignment explanation
Indices: 211993--212320 Score: 200
Period size: 61 Copynumber: 5.5 Consensus size: 61
211983 CACTTTTGTT
* * * *
211993 ATCTTTAAG-CCTAATATCGCTGGCCTTGAATTAGCA-TTTTGACACCTTTATCATTCTTCTC
1 ATCTTTAAGTCC-AATATCGCTGGCCTTGAATCATCACATTAG-CACCTTTATCATTCTTCTC
* * * *
212054 ATCTTTAAGTCCAATGTCGTTGGCTTTGAATCATCACATTAGCA-C-----C--T-TTGTC
1 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCATCACATTAGCACCTTTATCATTCTTCTC
* * * * *
212106 ATGTTTAAG-CCTAATATCGTTGGCCTTGAATTAGCATATTAGCACCTTTATCATTCTTCTC
1 ATCTTTAAGTCC-AATATCGCTGGCCTTGAATCATCACATTAGCACCTTTATCATTCTTCTC
* * * * * * * *
212167 ATCTTCAAGCCCGATATCACTGGCCGTGAATCAACATATTGGCACCTTTATCATTCTT-TGC
1 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCATCACATTAGCACCTTTATCATTCTTCT-C
* * * * * * * *
212228 ATCTTTAACTCCAATGTCGCTGACCTTGAATCAGT-ACATTGGCATTCTTT-TTATCCTTATC
1 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCA-TCACATTAGCA-CCTTTATCATTCTTCTC
* * * *
212289 ATCTTTAAGTCTAGTATTGCAGGCCTTGAATC
1 ATCTTTAAGTCCAATATCGCTGGCCTTGAATC
212321 TAGACACTAG
Statistics
Matches: 206, Mismatches: 44, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
51 2 0.01
52 39 0.19
53 2 0.01
55 1 0.00
58 1 0.00
60 3 0.01
61 146 0.71
62 12 0.06
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.39
Consensus pattern (61 bp):
ATCTTTAAGTCCAATATCGCTGGCCTTGAATCATCACATTAGCACCTTTATCATTCTTCTC
Found at i:212212 original size:113 final size:113
Alignment explanation
Indices: 211824--212225 Score: 452
Period size: 113 Copynumber: 3.5 Consensus size: 113
211814 TCCAATATCG
* * * * *
211824 CTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACAGATTGGCATCTTTGTCATTTTTTTTA
1 CTCATCTTCAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTTGTCA--TCTTTAA
* * * * *
211889 GTCC-AATATCATTGGCCTTGAATCAACATA-TCG-ACATTTTATCATTCTT
64 G-CCTAATATCGTTGGCCTTGAATTAGCATATTAGCAC-CTTTATCATTCTT
* * * * *
211938 CTCATTTTCAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTGTTATCTTTAAGC
1 CTCATCTTCAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTTGTCATCTTTAAGC
* *
212003 CTAATATCGCTGGCCTTGAATTAGCAT-TTTGACACCTTTATCATTCTT
66 CTAATATCGTTGGCCTTGAATTAGCATATTAG-CACCTTTATCATTCTT
* * * * * * *
212051 CTCATCTTTAAGTCCAATGTCGTTGGCTTTGAATCATCACATTAGCACCTTTGTCATGTTTAAGC
1 CTCATCTTCAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTTGTCATCTTTAAGC
212116 CTAATATCGTTGGCCTTGAATTAGCATATTAGCACCTTTATCATTCTT
66 CTAATATCGTTGGCCTTGAATTAGCATATTAGCACCTTTATCATTCTT
* * * * * *
212164 CTCATCTTCAAGCCCGATATCACTGGCCGTGAATCAACATATTGGCACCTTTATCATTCTTT
1 CTCATCTTCAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTTGTCA-TCTTT
212226 GCATCTTTAA
Statistics
Matches: 242, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
111 2 0.01
112 29 0.12
113 154 0.64
114 57 0.24
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.39
Consensus pattern (113 bp):
CTCATCTTCAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTTGTCATCTTTAAGC
CTAATATCGTTGGCCTTGAATTAGCATATTAGCACCTTTATCATTCTT
Found at i:215882 original size:17 final size:17
Alignment explanation
Indices: 215862--215898 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
215852 CTAGACAAAG
215862 AATTTGTACAAACAAGA
1 AATTTGTACAAACAAGA
215879 AATTTGTACAAACAAGA
1 AATTTGTACAAACAAGA
215896 AAT
1 AAT
215899 GCCTCTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (17 bp):
AATTTGTACAAACAAGA
Found at i:216315 original size:20 final size:20
Alignment explanation
Indices: 216290--216355 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
216280 TATCGATATA
216290 ATGTATCGATACATTGTCCT
1 ATGTATCGATACATTGTCCT
*
216310 ATGTATCGAT--A---T--A
1 ATGTATCGATACATTGTCCT
216323 ATGTATCGATACATTGTCCT
1 ATGTATCGATACATTGTCCT
216343 ATGTATCGATACA
1 ATGTATCGATACA
216356 AATAGTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
15 2 0.05
18 2 0.05
20 23 0.62
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTCCT
Found at i:216319 original size:33 final size:33
Alignment explanation
Indices: 216255--216353 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
216245 TGTTACAAGC
*
216255 AATGTATCGATACAATT-TCATCATGTATCGATAT
1 AATGTATCGATAC-ATTGTCCT-ATGTATCGATAT
216289 AATGTATCGATACATTGTCCTATGTATCGATAT
1 AATGTATCGATACATTGTCCTATGTATCGATAT
216322 AATGTATCGATACATTGTCCTATGTATCGATA
1 AATGTATCGATACATTGTCCTATGTATCGATA
216354 CAAATAGTGA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
33 47 0.75
34 16 0.25
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (33 bp):
AATGTATCGATACATTGTCCTATGTATCGATAT
Found at i:216443 original size:13 final size:13
Alignment explanation
Indices: 216425--216451 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
216415 TACAATAAGC
216425 ATGTATCGATATA
1 ATGTATCGATATA
216438 ATGTATCGATATA
1 ATGTATCGATATA
216451 A
1 A
216452 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:217041 original size:22 final size:21
Alignment explanation
Indices: 216980--217048 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
216970 TTTCGTTTTA
216980 CTCCCCCTTAATTAAAGAATTT
1 CTCCCCCTTAA-TAAAGAATTT
*
217002 CT-CTCCTT--TAAA-AA-TT
1 CTCCCCCTTAATAAAGAATTT
217018 CTCCCCCTTAATCAAAGAATTT
1 CTCCCCCTTAAT-AAAGAATTT
217040 CTCCCCCTT
1 CTCCCCCTT
217049 TGTCAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
16 4 0.10
17 7 0.18
18 4 0.10
19 1 0.03
20 3 0.08
21 7 0.18
22 13 0.33
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (21 bp):
CTCCCCCTTAATAAAGAATTT
Found at i:218969 original size:27 final size:27
Alignment explanation
Indices: 218931--219026 Score: 174
Period size: 27 Copynumber: 3.6 Consensus size: 27
218921 TACAAGGAAT
218931 GTTGTATCGATACATCTGGGTTTTCCA
1 GTTGTATCGATACATCTGGGTTTTCCA
218958 GTTGTATCGATACATCTGGGTTTTCCA
1 GTTGTATCGATACATCTGGGTTTTCCA
*
218985 GTTGTATCGATACATCTGGTTTTTCCA
1 GTTGTATCGATACATCTGGGTTTTCCA
*
219012 GATGTATCGATACAT
1 GTTGTATCGATACAT
219027 GTCTCTATGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
GTTGTATCGATACATCTGGGTTTTCCA
Found at i:224961 original size:13 final size:13
Alignment explanation
Indices: 224920--224968 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
224910 TCGTTACAAG
224920 CAATGTATCGATA
1 CAATGTATCGATA
224933 CAAT-T-TC-AT-
1 CAATGTATCGATA
224942 C-ATGTATCGATA
1 CAATGTATCGATA
224954 CAATGTATCGATA
1 CAATGTATCGATA
224967 CA
1 CA
224969 TTGTCCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:224963 original size:34 final size:33
Alignment explanation
Indices: 224920--224989 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
224910 TCGTTACAAG
224920 CAATGTATCGATACAATT-TCATCATGTATCGATA
1 CAATGTATCGATAC-ATTGTCAT-ATGTATCGATA
*
224954 CAATGTATCGATACATTGTCCTATGTATCGATA
1 CAATGTATCGATACATTGTCATATGTATCGATA
224987 CAA
1 CAA
224990 ACAGTGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (33 bp):
CAATGTATCGATACATTGTCATATGTATCGATA
Found at i:225057 original size:13 final size:13
Alignment explanation
Indices: 225039--225065 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
225029 ACAATTGTCT
225039 ATGTATCGATACA
1 ATGTATCGATACA
225052 ATGTATCGATACA
1 ATGTATCGATACA
225065 A
1 A
225066 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:226364 original size:55 final size:55
Alignment explanation
Indices: 226298--226407 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
226288 ATACAAATGA
226298 ATTAACTAAGCCGAACAAGGAAAAAGAAAGAAAACGTAATAGTCGTAATGTATCT
1 ATTAACTAAGCCGAACAAGGAAAAAGAAAGAAAACGTAATAGTCGTAATGTATCT
226353 ATTAACTAAGCCGAACAAGGAAAAAGAAAGAAAACGTAATAGTCGTAATGTATCT
1 ATTAACTAAGCCGAACAAGGAAAAAGAAAGAAAACGTAATAGTCGTAATGTATCT
226408 CGTAATTACC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (55 bp):
ATTAACTAAGCCGAACAAGGAAAAAGAAAGAAAACGTAATAGTCGTAATGTATCT
Found at i:228592 original size:33 final size:33
Alignment explanation
Indices: 228537--228602 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
228527 AAATTCCCAG
* *
228537 ATGTATCGATACAAAGATTAATGTATTGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
* **
228570 ATGTATCGATATATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
228603 TTTCTTTGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:229083 original size:13 final size:13
Alignment explanation
Indices: 229065--229089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229055 GCATTTAATA
229065 CCCATTAATGCCC
1 CCCATTAATGCCC
229078 CCCATTAATGCC
1 CCCATTAATGCC
229090 TCCACCCATA
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:0.24, C:0.44, G:0.08, T:0.24
Consensus pattern (13 bp):
CCCATTAATGCCC
Found at i:236068 original size:166 final size:163
Alignment explanation
Indices: 235756--236101 Score: 398
Period size: 166 Copynumber: 2.1 Consensus size: 163
235746 CATCTTTCCT
* * * *
235756 TTTATTTAATGAATTTTTATTTTTTCTTGAAATTTCTCTATTTTCGAAATACGGAGTTTTCTACT
1 TTTATTTCATGAATTTTTATTTTTTCTTGAAAATTCTCTATTTTCAAAATACGAAGTTTTCTACT
* * * *
235821 CCGTAAATGTTTTCGGGGGATTTTTCTTGATTTATAATTTTTAAAATTCATCAAATATCATCATT
66 CCATAAATGTTTTCGGGGGATTTTTCTCGATTTAAAATTTTTAAAATTCATCAAACATCATCATT
* *
235886 TAATTCATAGTAAATCAGTTTT-GAAAATTC-A
131 TAATCCATAGTAAATCAATTTTGGAAAATTCAA
*
235917 TTTATTTTCATGAATTTTTCATTTTTTTCTTTAAAATTCTCCTATTTTCATAAA-ATC-AAGTTT
1 TTTA-TTTCATGAATTTTT-A-TTTTTTCTTGAAAATTCT-CTATTTTCA-AAATA-CGAAGTTT
* * * *
235980 TCTATTTCATAAATGTTTTCGAGGGGATTTTTCTCGATTTAAAATTTTTTAAATTCATCTAACAT
60 TCTACTCCATAAATGTTTTCG-GGGGATTTTTCTCGATTTAAAATTTTTAAAATTCATCAAACAT
** * *
236045 TGTCA-TTAGACTCCCT-TTAAATCAATTTTGGAAAATTCAA
124 CATCATTTA-A-TCCATAGTAAATCAATTTTGGAAAATTCAA
236085 TTTATTTCATGAATTTT
1 TTTATTTCATGAATTTT
236102 GTAAAACATT
Statistics
Matches: 155, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
161 4 0.03
162 13 0.08
163 1 0.01
164 16 0.10
165 35 0.23
166 57 0.37
167 24 0.15
168 5 0.03
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (163 bp):
TTTATTTCATGAATTTTTATTTTTTCTTGAAAATTCTCTATTTTCAAAATACGAAGTTTTCTACT
CCATAAATGTTTTCGGGGGATTTTTCTCGATTTAAAATTTTTAAAATTCATCAAACATCATCATT
TAATCCATAGTAAATCAATTTTGGAAAATTCAA
Found at i:238473 original size:19 final size:20
Alignment explanation
Indices: 238449--238502 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
238439 ACTTTATGCT
**
238449 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCACAA
238468 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
238488 TTGTATCGATACATG
1 TTGTATCGATACATG
238503 AAACTAGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:245525 original size:33 final size:34
Alignment explanation
Indices: 245488--245555 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
245478 TGAGAGTTGA
*
245488 TCACTTTACTTTCACAA-CACAT-GAGTGAGCACT
1 TCACTTCACTTTCACAAGCACATGGA-TGAGCACT
*
245521 TCACTTCACTTTCACAAGCGCATGGATGAGCACT
1 TCACTTCACTTTCACAAGCACATGGATGAGCACT
245555 T
1 T
245556 TGGTGCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 16 0.52
34 13 0.42
35 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (34 bp):
TCACTTCACTTTCACAAGCACATGGATGAGCACT
Found at i:245935 original size:30 final size:33
Alignment explanation
Indices: 245858--245938 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 33
245848 AAATAAATTT
* * * *
245858 TTATCAAAGAGGAAAAAATTTTTTAAACGATTA
1 TTATCAAGGGGGAGAAAATCTTTTAAACGATTA
*
245891 TTAATCAATGGGGAGAAAATCTTTTAAACGATTA
1 TT-ATCAAGGGGGAGAAAATCTTTTAAACGATTA
245925 -T-T-AAGGGGGAGAAA
1 TTATCAAGGGGGAGAAA
245939 TTTTTTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 11 0.26
31 1 0.02
33 3 0.07
34 27 0.64
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (33 bp):
TTATCAAGGGGGAGAAAATCTTTTAAACGATTA
Found at i:246617 original size:13 final size:13
Alignment explanation
Indices: 246599--246625 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
246589 ACATTATGCT
246599 TTGTATCGATACA
1 TTGTATCGATACA
246612 TTGTATCGATACA
1 TTGTATCGATACA
246625 T
1 T
246626 GCACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:246717 original size:20 final size:20
Alignment explanation
Indices: 246675--246728 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
246665 CTACCACTGT
*
246675 TTGTATCAATACATGGGACA
1 TTGTATCAATACATAGGACA
*
246695 TTGTATCAATACATAATGA-A
1 TTGTATCAATACAT-AGGACA
*
246715 TTGTATCGATACAT
1 TTGTATCAATACAT
246729 TGCTTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCAATACATAGGACA
Found at i:250666 original size:13 final size:13
Alignment explanation
Indices: 250648--250672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
250638 AAATTGCTTA
250648 GTATCGATACATT
1 GTATCGATACATT
250661 GTATCGATACAT
1 GTATCGATACAT
250673 GTTCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:258470 original size:10 final size:11
Alignment explanation
Indices: 258448--258477 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
258438 ATTAAGATAA
258448 TAATTTTTATT
1 TAATTTTTATT
258459 TAATTTTT-TT
1 TAATTTTTATT
258469 TAATTTTTA
1 TAATTTTTA
258478 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TAATTTTTATT
Found at i:258750 original size:2 final size:2
Alignment explanation
Indices: 258743--258775 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
258733 AATAATAGAA
*
258743 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
258776 AATGATTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:259570 original size:13 final size:11
Alignment explanation
Indices: 259528--259580 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
259518 AACTTAACTA
259528 CTTTTTTTT-T
1 CTTTTTTTTCT
*
259538 CTTATTTTCTCT
1 CTT-TTTTTTCT
* *
259550 CGTTTTCTT-T
1 CTTTTTTTTCT
259560 CTTTTTTTTCT
1 CTTTTTTTTCT
259571 CTTTTTTTTC
1 CTTTTTTTTC
259581 ACTGGCCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 11 0.32
11 20 0.59
12 3 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (11 bp):
CTTTTTTTTCT
Found at i:260355 original size:159 final size:162
Alignment explanation
Indices: 260102--260395 Score: 371
Period size: 163 Copynumber: 1.8 Consensus size: 162
260092 AATGGTAATA
*
260102 TTAGATAAATTTTAAAAAATTTAAACAAAGAAAAATCCCCCCCCCCAAAATATTTATGGAATAGA
1 TTAGATAAATTTTAAAAAATTTAAACAAAGAAAAA---CCCCCCCCAAAATATTTATAGAATAGA
* *** * *
260167 AAACTTAGTTTTTTGGAAACAAGAAAATTT-TA-AAAAAT-GAAAACTAATAAAAATAAATGAAT
63 AAACTTAATTTTTCAAAAACAAGAAAATTTAAAGAAAAATAAAAAACTAATAAAAATAAAT-AAT
260229 TTTTTAAATTGATTTAAAGGGAGTCTAATGACAATG
127 TTTTTAAATTGATTTAAAGGGAGTCTAATGACAATG
* * * * *
260265 TTAGATAAATTTTAAAAATTTTAAATAGAGAAAAA-CCTCCCGAAAATATTTATAGAATAGAAAA
1 TTAGATAAATTTTAAAAAATTTAAACAAAGAAAAACCCCCCCCAAAATATTTATAGAATAGAAAA
* * * *
260329 CTTAATTTTTCAAAAATAAGAGAATTTCAAAGAAAAATAAAAAACTTATGAAAATAAATAATTTT
66 CTTAATTTTTCAAAAACAAGAAAATTT-AAAGAAAAATAAAAAACTAATAAAAATAAATAATTTT
260394 TT
130 TT
260396 CAAAAACTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
159 47 0.42
161 1 0.01
162 14 0.13
163 49 0.44
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.31
Consensus pattern (162 bp):
TTAGATAAATTTTAAAAAATTTAAACAAAGAAAAACCCCCCCCAAAATATTTATAGAATAGAAAA
CTTAATTTTTCAAAAACAAGAAAATTTAAAGAAAAATAAAAAACTAATAAAAATAAATAATTTTT
TAAATTGATTTAAAGGGAGTCTAATGACAATG
Found at i:273934 original size:39 final size:39
Alignment explanation
Indices: 273861--274012 Score: 141
Period size: 39 Copynumber: 3.9 Consensus size: 39
273851 ATCATATTTA
273861 TTTAA-AAAAAATTTATGTATTAGTC-TCA-CTTTTTA-AT
1 TTTAATAAAAAATTTATGTATTAGTCAT-ATC-TTTTAGAT
273898 TTTAATAAAAAAATTTATGTATTAGTCATATCTTTTAGAT
1 TTTAAT-AAAAAATTTATGTATTAGTCATATCTTTTAGAT
* * ** * * *
273938 TCTAATAAATAATTTATACATTACTAATATCTTTTAGAA
1 TTTAATAAAAAATTTATGTATTAGTCATATCTTTTAGAT
* * * * *
273977 GTCAGTAAAAAATTCATGTATTAGTCATATATTTTA
1 TTTAATAAAAAATTTATGTATTAGTCATATCTTTTA
274013 AACTTAAGTT
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
37 5 0.05
39 78 0.85
40 9 0.10
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (39 bp):
TTTAATAAAAAATTTATGTATTAGTCATATCTTTTAGAT
Found at i:274391 original size:88 final size:87
Alignment explanation
Indices: 274240--274409 Score: 254
Period size: 88 Copynumber: 1.9 Consensus size: 87
274230 TCAATACATG
* *
274240 TTAAGAAATCGCCAGTCTTAATTGACGATTTCTCATCTATATTACAAATTTATCTTCTCAAAAAA
1 TTAAGAAATCGCCACTCTTAATTGACGATTTCTCATCTATATTACAAATTTATATTCTC--AAAA
274305 AATAATTTTTTAATAAATTCAGAC
64 AATAATTTTTTAATAAATTCAGAC
* * *
274329 TTAAGAAATCGTCACT-TTAATTGACGATTTCTCATTTATATTATAAATTTATATTCAT-AAAAA
1 TTAAGAAATCGCCACTCTTAATTGACGATTTCTCATCTATATTACAAATTTATATTC-TCAAAAA
274392 ATAATTTTTTAATAAATT
65 ATAATTTTTTAATAAATT
274410 TATAAAAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
86 23 0.31
88 37 0.49
89 15 0.20
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (87 bp):
TTAAGAAATCGCCACTCTTAATTGACGATTTCTCATCTATATTACAAATTTATATTCTCAAAAAA
TAATTTTTTAATAAATTCAGAC
Found at i:274427 original size:26 final size:27
Alignment explanation
Indices: 274379--274443 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
274369 TTATAAATTT
* * *
274379 ATATTCATAAAAAATAATTTTTTAATA
1 ATATTTATAAAAAATAATATTTTAAAA
274406 A-ATTTATAAAAAA-ACATATTTTAAAA
1 ATATTTATAAAAAATA-ATATTTTAAAA
*
274432 ATATTTTTAAAA
1 ATATTTATAAAA
274444 TTAAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 21 0.66
27 10 0.31
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTTATAAAAAATAATATTTTAAAA
Found at i:277076 original size:1 final size:1
Alignment explanation
Indices: 277070--277102 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
277060 ATTATAGTAG
277070 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
277103 AAGTATATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:278612 original size:18 final size:18
Alignment explanation
Indices: 278591--278653 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
278581 ACGCTGAAGA
278591 TGAGGGTGATGGAGAGGC
1 TGAGGGTGATGGAGAGGC
* ** * *
278609 TGAGGGTGAAGCTGAAGA
1 TGAGGGTGATGGAGAGGC
278627 TGAGGGTGATGGAGAGGC
1 TGAGGGTGATGGAGAGGC
278645 TGAGGGTGA
1 TGAGGGTGA
278654 AGATGAAGGA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.25, C:0.05, G:0.52, T:0.17
Consensus pattern (18 bp):
TGAGGGTGATGGAGAGGC
Found at i:278613 original size:36 final size:36
Alignment explanation
Indices: 278573--278674 Score: 143
Period size: 36 Copynumber: 2.8 Consensus size: 36
278563 AAAATGAGAG
*
278573 TGAGGATGACGCTGAAGATGAGGGTGATGGAGAGGC
1 TGAGGATGAAGCTGAAGATGAGGGTGATGGAGAGGC
*
278609 TGAGGGTGAAGCTGAAGATGAGGGTGATGGAGAGGC
1 TGAGGATGAAGCTGAAGATGAGGGTGATGGAGAGGC
* * *
278645 TGAGGGTGAAGATGAAGGA-GAGGATGATGG
1 TGAGGATGAAGCTGAA-GATGAGGGTGATGG
278675 TGATGATGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 59 0.97
37 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.49, T:0.17
Consensus pattern (36 bp):
TGAGGATGAAGCTGAAGATGAGGGTGATGGAGAGGC
Found at i:278664 original size:24 final size:24
Alignment explanation
Indices: 278637--278685 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
278627 TGAGGGTGAT
*
278637 GGAGAGGCTGAGGGTGAAGATGAA
1 GGAGAGGATGAGGGTGAAGATGAA
* *
278661 GGAGAGGATGATGGTGATGATGAA
1 GGAGAGGATGAGGGTGAAGATGAA
278685 G
1 G
278686 ATGGTGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.49, T:0.16
Consensus pattern (24 bp):
GGAGAGGATGAGGGTGAAGATGAA
Found at i:284574 original size:16 final size:16
Alignment explanation
Indices: 284542--284628 Score: 104
Period size: 16 Copynumber: 5.4 Consensus size: 16
284532 TAAAATTTTT
284542 GAGTCATTTTCGGGTTC
1 GAGTCATTTT-GGGTTC
**
284559 GAGTTGTTTTGGGTTC
1 GAGTCATTTTGGGTTC
*
284575 GAATCATTTTGGGTTC
1 GAGTCATTTTGGGTTC
284591 G-GATCATTTTGGGTTC
1 GAG-TCATTTTGGGTTC
*
284607 GAGTCATTTTGGATTC
1 GAGTCATTTTGGGTTC
*
284623 GGGTCA
1 GAGTCA
284629 ATCGAGTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
16 51 0.85
17 9 0.15
ACGTcount: A:0.14, C:0.13, G:0.31, T:0.43
Consensus pattern (16 bp):
GAGTCATTTTGGGTTC
Found at i:285477 original size:32 final size:32
Alignment explanation
Indices: 285441--285502 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
285431 TTTAAGTTCA
*
285441 GTCATTTCGAGTTTGGATTATTTTGGGTTTGG
1 GTCATTTCAAGTTTGGATTATTTTGGGTTTGG
* * * *
285473 GTCATTTTAAGTTTGGGTTGTTTTTGGTTT
1 GTCATTTCAAGTTTGGATTATTTTGGGTTT
285503 TGGATTGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.11, C:0.05, G:0.29, T:0.55
Consensus pattern (32 bp):
GTCATTTCAAGTTTGGATTATTTTGGGTTTGG
Found at i:285479 original size:16 final size:16
Alignment explanation
Indices: 285441--285490 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
285431 TTTAAGTTCA
*
285441 GTCATTTCGAGTTTGG
1 GTCATTTTGAGTTTGG
* * *
285457 ATTATTTTGGGTTTGG
1 GTCATTTTGAGTTTGG
*
285473 GTCATTTTAAGTTTGG
1 GTCATTTTGAGTTTGG
285489 GT
1 GT
285491 TGTTTTTGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.14, C:0.06, G:0.30, T:0.50
Consensus pattern (16 bp):
GTCATTTTGAGTTTGG
Found at i:285502 original size:16 final size:16
Alignment explanation
Indices: 285451--285502 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
285441 GTCATTTCGA
* *
285451 GTTTGGATTATTTTGG
1 GTTTGGGTTATTTTAG
* *
285467 GTTTGGGTCATTTTAA
1 GTTTGGGTTATTTTAG
* *
285483 GTTTGGGTTGTTTTTG
1 GTTTGGGTTATTTTAG
285499 GTTT
1 GTTT
285503 TGGATTGGTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.10, C:0.02, G:0.31, T:0.58
Consensus pattern (16 bp):
GTTTGGGTTATTTTAG
Found at i:285513 original size:21 final size:21
Alignment explanation
Indices: 285488--285532 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
285478 TTTAAGTTTG
*
285488 GGTTGTTTTTGGTTTTGGATT
1 GGTTGTTTTTGGGTTTGGATT
285509 GGTTGTTTTTGGGTTTGGATT
1 GGTTGTTTTTGGGTTTGGATT
285530 GGT
1 GGT
285533 CGGTTTCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.00, G:0.38, T:0.58
Consensus pattern (21 bp):
GGTTGTTTTTGGGTTTGGATT
Found at i:285538 original size:22 final size:21
Alignment explanation
Indices: 285492--285538 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
285482 AGTTTGGGTT
* *
285492 GTTTTTGGTTTTGGATTGGTT
1 GTTTTTGGGTTTGGATTGGTG
285513 GTTTTTGGGTTTGGATTGGTCG
1 GTTTTTGGGTTTGGATTGGT-G
285535 GTTT
1 GTTT
285539 CGGGTTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.04, C:0.02, G:0.36, T:0.57
Consensus pattern (21 bp):
GTTTTTGGGTTTGGATTGGTG
Found at i:285543 original size:21 final size:21
Alignment explanation
Indices: 285501--285544 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
285491 TGTTTTTGGT
* * *
285501 TTTGGATTGGTTGTTTTTGGG
1 TTTGGATTGGTCGGTTTCGGG
285522 TTTGGATTGGTCGGTTTCGGG
1 TTTGGATTGGTCGGTTTCGGG
285543 TT
1 TT
285545 GTTGATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.05, G:0.39, T:0.52
Consensus pattern (21 bp):
TTTGGATTGGTCGGTTTCGGG
Found at i:287345 original size:13 final size:14
Alignment explanation
Indices: 287317--287351 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
287307 TTATAAATAA
287317 TAAATTTAGATATT
1 TAAATTTAGATATT
*
287331 TAAATTT-GTTATT
1 TAAATTTAGATATT
287344 TAAATTTA
1 TAAATTTA
287352 TTTTACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
TAAATTTAGATATT
Found at i:287661 original size:229 final size:229
Alignment explanation
Indices: 287260--287712 Score: 852
Period size: 229 Copynumber: 2.0 Consensus size: 229
287250 ATTAGAAGTT
287260 GTTGCAACAATGAGTTTATAAATATCAATTATTGGAATTCGTACTATTTATAAATAATAAATTTA
1 GTTGCAACAATGAGTTTATAAATATCAATTATTGGAATTCGTACTATTTATAAATAATAAATTTA
*
287325 GATATTTAAATTTGTTATTTAAATTTATTTTACTTTTATAGATAATAAATTTAAATATTAATATT
66 GATATTTAAATTTGTTATTTAAATTTATTTTACTTTTATAAATAATAAATTTAAATATTAATATT
* *
287390 TAAATTTATTTTTGATTTATTTATAAAATGTAAAAATTTATGTACATGAAAAGAATTGAATCTTA
131 TAAATTTATTTTTGATTTATTTATAAAATATAAAAATTTATGTACATGAAAAGAATTGAACCTTA
287455 GTTAATAAAATTAATTAATAAGAATTTTATAGTG
196 GTTAATAAAATTAATTAATAAGAATTTTATAGTG
* *
287489 GTTGCAACAATGAGTTTATAAATATCAATTATTTGAATTCGTACTATTTATAAATAATAGATTTA
1 GTTGCAACAATGAGTTTATAAATATCAATTATTGGAATTCGTACTATTTATAAATAATAAATTTA
*
287554 GATATTTAAATTTGTTATTTAAATTTATTTTATTTTTATAAATAATAAATTTAAATATTAATATT
66 GATATTTAAATTTGTTATTTAAATTTATTTTACTTTTATAAATAATAAATTTAAATATTAATATT
287619 TAAATTTATTTTTGATTTATTTATAAAATATAAAAATTTATGTACATGAAAAGAATTGAACCTTA
131 TAAATTTATTTTTGATTTATTTATAAAATATAAAAATTTATGTACATGAAAAGAATTGAACCTTA
287684 GTTAATAAAATTAATTAATAAGAATTTTA
196 GTTAATAAAATTAATTAATAAGAATTTTA
287713 CCAAGTGAAC
Statistics
Matches: 218, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
229 218 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (229 bp):
GTTGCAACAATGAGTTTATAAATATCAATTATTGGAATTCGTACTATTTATAAATAATAAATTTA
GATATTTAAATTTGTTATTTAAATTTATTTTACTTTTATAAATAATAAATTTAAATATTAATATT
TAAATTTATTTTTGATTTATTTATAAAATATAAAAATTTATGTACATGAAAAGAATTGAACCTTA
GTTAATAAAATTAATTAATAAGAATTTTATAGTG
Found at i:295867 original size:78 final size:77
Alignment explanation
Indices: 295737--296022 Score: 268
Period size: 79 Copynumber: 3.6 Consensus size: 77
295727 TTATTCATGT
* ** * * *
295737 TTTTATTTCTAAAACATCGATTTTTCACAATCGATGATACTTTAATCTCGTTA-TTTCTAAGGGG
1 TTTTATTTCTAAAACATC-AATTTTCACAATCGA-GATACTCCAACCCCGTTAGTTT-TGAGGGG
* ***
295801 ATACTCCAATCCTGG
63 ATACTCCAAGCCCCA
*
295816 TTTTATTTCTAAAACATTAATTTTCACAATCGAGAATACTCCAACCCCGTTAGTTTTGAGGGGAT
1 TTTTATTTCTAAAACATCAATTTTCACAATCGAG-ATACTCCAACCCCGTTAGTTTTGAGGGGAT
*
295881 ACTCTAAGCCCCA
65 ACTCCAAGCCCCA
* * * * * *
295894 CTTTATTTCTAAAATATCGATTTTCCATAATTGGGGATACTCCAACCCCGTTAGTTTTGAGGGGA
1 TTTTATTTCTAAAACATCAATTTT-CACAA-TCGAGATACTCCAACCCCGTTAGTTTTGAGGGGA
*
295959 TACTCTAAGCCCCA
64 TACTCCAAGCCCCA
* * * * * *
295973 CTTTATTTCTAAAATATCGATTTTCCATAATTGGGGATACTCCAACCCCG
1 TTTTATTTCTAAAACATCAATTTT-CACAA-TCGAGATACTCCAACCCCG
296023 GCTTTATTTC
Statistics
Matches: 184, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
77 1 0.01
78 63 0.34
79 117 0.64
80 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (77 bp):
TTTTATTTCTAAAACATCAATTTTCACAATCGAGATACTCCAACCCCGTTAGTTTTGAGGGGATA
CTCCAAGCCCCA
Found at i:295959 original size:79 final size:79
Alignment explanation
Indices: 295851--296022 Score: 344
Period size: 79 Copynumber: 2.2 Consensus size: 79
295841 ACAATCGAGA
295851 ATACTCCAACCCCGTTAGTTTTGAGGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATT
1 ATACTCCAACCCCGTTAGTTTTGAGGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATT
295916 TTCCATAATTGGGG
66 TTCCATAATTGGGG
295930 ATACTCCAACCCCGTTAGTTTTGAGGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATT
1 ATACTCCAACCCCGTTAGTTTTGAGGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATT
295995 TTCCATAATTGGGG
66 TTCCATAATTGGGG
296009 ATACTCCAACCCCG
1 ATACTCCAACCCCG
296023 GCTTTATTTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 93 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (79 bp):
ATACTCCAACCCCGTTAGTTTTGAGGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATT
TTCCATAATTGGGG
Found at i:296030 original size:51 final size:51
Alignment explanation
Indices: 295954--296073 Score: 188
Period size: 51 Copynumber: 2.4 Consensus size: 51
295944 TTAGTTTTGA
* *
295954 GGGGATACTCTAAGCCCC-ACTTTATTTCTAAAATATCGATTTTCCATAATT
1 GGGGATACTCCAA-CCCCGACTTTATTTCTAAAATATCAATTTTCCATAATT
* *
296005 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATCAATTTTTCATAATT
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAATATCAATTTTCCATAATT
296056 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
296074 TTATTTCTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 4 0.06
51 60 0.94
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCTAAAATATCAATTTTCCATAATT
Found at i:296091 original size:79 final size:79
Alignment explanation
Indices: 296008--296158 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 79
295998 CATAATTGGG
* * * *
296008 GATACTCCAACCCCGGCTTTATTTCTAAAATATCAATTTTTCATAATTGGGGATACTCC-AACCC
1 GATACTCCAACCCCAGCTTTATTTCCAAAACATCAATTTTTCACAATTGGGGATAC-CCAAACCC
296072 CGTTATTTCTGAATA
65 CGTTATTTCTGAATA
* * * * * *
296087 GATACTCCAACCCTAGTTTTATTTCCAAAACATCGATTTTTTACCATTGGGGATACCCAAACCCT
1 GATACTCCAACCCCAGCTTTATTTCCAAAACATCAATTTTTCACAATTGGGGATACCCAAACCCC
296152 GTTATTT
66 GTTATTT
296159 TCGACTCTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
78 2 0.03
79 59 0.97
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (79 bp):
GATACTCCAACCCCAGCTTTATTTCCAAAACATCAATTTTTCACAATTGGGGATACCCAAACCCC
GTTATTTCTGAATA
Found at i:296108 original size:130 final size:130
Alignment explanation
Indices: 295875--296126 Score: 348
Period size: 130 Copynumber: 1.9 Consensus size: 130
295865 TTAGTTTTGA
* *
295875 GGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATTTTCCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAAGCCCCACTTTATTTCTAAAATATCAATTTTCCATAATTGGGGATACTCCAAC
* * * * *
295940 CCCGTTAGTTTTGAGGGGATACTCTAAGCCCCACTTTATTTCTAAAATATCGATTTTCCATAATT
66 CCCGTTAGTTTTGAAGAGATACTCCAAGCCCCACTTTATTTCCAAAACATCGATTTTCCATAATT
* *
296005 GGGGATACTCCAA-CCCCGGCTTTATTTCTAAAATATCAATTTTTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAAGCCCC-ACTTTATTTCTAAAATATCAATTTTCCATAATTGGGGATACTCCAA
* * *
296069 CCCCGTTA-TTTCTGAATAGATACTCCAA-CCCTAGTTTTATTTCCAAAACATCGATTTT
65 CCCCGTTAGTTT-TGAAGAGATACTCCAAGCCCCA-CTTTATTTCCAAAACATCGATTTT
296127 TTACCATTGG
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
129 11 0.10
130 96 0.90
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (130 bp):
GGGGATACTCCAAGCCCCACTTTATTTCTAAAATATCAATTTTCCATAATTGGGGATACTCCAAC
CCCGTTAGTTTTGAAGAGATACTCCAAGCCCCACTTTATTTCCAAAACATCGATTTTCCATAATT
Found at i:309266 original size:52 final size:52
Alignment explanation
Indices: 309196--309316 Score: 181
Period size: 52 Copynumber: 2.3 Consensus size: 52
309186 GAAAATTTAC
* *
309196 CTGCACGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTG-
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGT
* * *
309247 CTTGGATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAATTTGT
1 C-TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGT
309300 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
309317 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
51 1 0.02
52 60 0.97
53 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGT
Found at i:309329 original size:52 final size:52
Alignment explanation
Indices: 309188--309336 Score: 160
Period size: 52 Copynumber: 2.9 Consensus size: 52
309178 CGAAATATGA
* * * *
309188 AAATTTACCTGCACGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGC
* *** * *
309240 AAATTTGCTTGGATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCTTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
309292 AAATTTG-TCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCT-TGCATGTATCGATACATAAGAT-AGTGTATCGATACA
309337 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 5 0.06
52 77 0.94
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCTTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
Found at i:309343 original size:13 final size:13
Alignment explanation
Indices: 309325--309383 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
309315 CAAAGATCAG
309325 TGTATCGATACAA
1 TGTATCGATACAA
309338 TGTATCGATAC-A
1 TGTATCGATACAA
309350 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
309359 TGTATCGATACAA
1 TGTATCGATACAA
309372 TGTATCGATACA
1 TGTATCGATACA
309384 TTTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:309368 original size:34 final size:34
Alignment explanation
Indices: 309325--309404 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
309315 CAAAGATCAG
309325 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
309359 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
309393 TGTATCGATACA
1 TGTATCGATACA
309405 TTTTTTGGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Found at i:309461 original size:33 final size:33
Alignment explanation
Indices: 309424--309490 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
309414 AGTAGCTTAA
309424 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
309457 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
309490 A
1 A
309491 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:309464 original size:13 final size:13
Alignment explanation
Indices: 309446--309470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
309436 CAAAAAAATA
309446 TGTATCGATACAT
1 TGTATCGATACAT
309459 TGTATCGATACA
1 TGTATCGATACA
309471 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:313224 original size:61 final size:61
Alignment explanation
Indices: 313127--313530 Score: 514
Period size: 61 Copynumber: 6.7 Consensus size: 61
313117 CTTTTATCCT
* *
313127 TTTTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATC
1 TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATC
* * *
313188 TTTTAGTCCTCAAAGAGCAGGACACCTTCTCTTTTTAAAGCACACACAAGTTGGTGGCA-C
1 TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * * * * * *
313248 ATTTCAGTCTTCAAAGAGCATGAC-ACTT-TCCTTTTAAAGCCCACACAAGTTGGAGGCAAC
1 -TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
313308 TTTTAGTCCCCAAAGAGTAGGAC-ACTTCT-TTTTTAAAGCCCACACAAGCTGGTGGCACC
1 TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATC
* ** *
313367 TTTTAGTTCTCAAAGACCAGGACGCCTTCTCTTTTTAAAGCCCATACAAGTTGGTGGCATC
1 TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATC
* * *
313428 TTTTAGTCCTCAAAAAGTAGGATGCCTTCT-TCTTTTAAAGCCCACACAAGTTAGTGGCATC
1 TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCT-TTTTAAAGCCCACACAAGTTGGTGGCATC
* *
313489 TTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCC
1 TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCC
313531 AAAGAGTAGG
Statistics
Matches: 298, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
59 94 0.32
60 12 0.04
61 192 0.64
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (61 bp):
TTTTAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATC
Found at i:313403 original size:120 final size:120
Alignment explanation
Indices: 313127--313530 Score: 544
Period size: 120 Copynumber: 3.4 Consensus size: 120
313117 CTTTTATCCT
* *
313127 TTTTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTT
* * *
313192 AGTCCTCAAAGAGCAGGACACCTTCTCTTTTTAAAGCACACACAAGTTGGTGGCACA
66 AGTCCTCAAAGAGTAGGACA-CTTCT-TTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * *
313249 TTTCAGTCTTCAAAGAGCATGAC-ACTT-TCCTTTTAAAGCCCACACAAGTTGGAGGCAACTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTT
* *
313312 AGTCCCCAAAGAGTAGGACACTTCTTTTTTAAAGCCCACACAAGCTGGTGGCACC
66 AGTCCTCAAAGAGTAGGACACTTCTTTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
313367 TTTTAGTTCTCAAAGACCAGGACGCCTTCTCTTTTTAAAGCCCATACAAGTTGGTGGCATCTTTT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTT
* * *
313432 AGTCCTCAAAAAGTAGGATGC-CTTCTTCTTTTAAAGCCCACACAAGTTAGTGGCATC
66 AGTCCTCAAAGAGTAGGA--CACTTCTT-TTTTAAAGCCCACACAAGTTGGTGGCACC
* *
313489 TTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCC
313531 AAAGAGTAGG
Statistics
Matches: 245, Mismatches: 32, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
118 45 0.18
119 8 0.03
120 100 0.41
121 9 0.04
122 83 0.34
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (120 bp):
TTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTT
AGTCCTCAAAGAGTAGGACACTTCTTTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:313535 original size:31 final size:31
Alignment explanation
Indices: 313499--313561 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
313489 TTTTAGTCCT
*
313499 CAAAGAGTAGGATGCCTTCTCCTTTTAAAGC
1 CAAAGAGTAGGACGCCTTCTCCTTTTAAAGC
* *
313530 CAAAGAGTAGGACGTCTTCTTCTTTTAAAGC
1 CAAAGAGTAGGACGCCTTCTCCTTTTAAAGC
313561 C
1 C
313562 TACACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (31 bp):
CAAAGAGTAGGACGCCTTCTCCTTTTAAAGC
Found at i:313611 original size:61 final size:59
Alignment explanation
Indices: 313530--313722 Score: 253
Period size: 61 Copynumber: 3.2 Consensus size: 59
313520 CTTTTAAAGC
* * * * *
313530 CAAAGAGTAGGACGTCTTCTTCTTTTAAAGCCTACACAAATTGGTGGCA-CTTTTCAATCCT
1 CAAAGAGCAGGAC-ACTTCTT-TTTTAAAGCCCACACAAATTGGTGGCACCTTCT-AGTCCT
* * *
313591 CAAAGAGCATGACACTTTCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCC
1 CAAAGAGCAGGACAC-TTC-TTTTTTAAAGCCCACACAAATTGGTGGCACCTTCTAGTCCT
*
313652 CAAAGAGCAGGACACTTCTTTTTTAAAGCCCACACAAACTGGTGGCACCTTCTAGTCCT
1 CAAAGAGCAGGACACTTCTTTTTTAAAGCCCACACAAATTGGTGGCACCTTCTAGTCCT
313711 CAAAGAGCAGGA
1 CAAAGAGCAGGA
313723 TGCCTCTCTC
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
59 50 0.43
60 4 0.03
61 57 0.49
62 6 0.05
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (59 bp):
CAAAGAGCAGGACACTTCTTTTTTAAAGCCCACACAAATTGGTGGCACCTTCTAGTCCT
Found at i:313617 original size:92 final size:92
Alignment explanation
Indices: 313438--313622 Score: 228
Period size: 92 Copynumber: 2.0 Consensus size: 92
313428 TTTTAGTCCT
* * *
313438 CAAAAAGTAGGATGCCTTCTTCTTTTAAAGCCCACACAAGTTAGTGGCATCTTTTAGTCCTCAAA
1 CAAAAAGTAGGACGCCTTCTTCTTTTAAAGCCCACACAAATTAGTGGCATCTTTTAATCCTCAAA
* **
313503 GAGTAGGATGCCTTCTCCTTTTAAAGC
66 GAGCAGGACACCTTCTCCTTTTAAAGC
* * * *
313530 CAAAGAGTAGGACGTCTTCTTCTTTTAAAGCCTACACAAATTGGTGGCA-CTTTTCAATCCTCAA
1 CAAAAAGTAGGACGCCTTCTTCTTTTAAAGCCCACACAAATTAGTGGCATCTTTT-AATCCTCAA
* * **
313594 AGAGCATGACACTTTCTTTTTTTAAAGC
65 AGAGCAGGACACCTTCTCCTTTTAAAGC
313622 C
1 C
313623 CACACAAGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
91 5 0.06
92 73 0.94
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (92 bp):
CAAAAAGTAGGACGCCTTCTTCTTTTAAAGCCCACACAAATTAGTGGCATCTTTTAATCCTCAAA
GAGCAGGACACCTTCTCCTTTTAAAGC
Found at i:313617 original size:153 final size:153
Alignment explanation
Indices: 313385--313663 Score: 373
Period size: 153 Copynumber: 1.8 Consensus size: 153
313375 CTCAAAGACC
* * * *
313385 AGGACGCCTTCTCTTTTTAAAGCCCATACAAGTTGGTGGCATCTTTTAGTCCTCAAAAAGTAGGA
1 AGGACGCCTTCTCTTTTTAAAGCCCACACAAATTGGTGGCATCTTTTAATCCTCAAAAAGCAGGA
** * * * *
313450 TGCCTTCTTCTTTTAAAGCCCACACAAGTTAGTGGCATCTTTTAGTCCTCAAAGAGTAGGATGCC
66 CACCTTCTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCTAGTCCCCAAAGAGCAGGATGCC
313515 TTCTCCTTTTAAAGCCAAAGAGT
131 TTCTCCTTTTAAAGCCAAAGAGT
* * * *
313538 AGGACGTCTTCT-TCTTTTAAAGCCTACACAAATTGGTGGCA-CTTTTCAATCCTCAAAGAGCAT
1 AGGACGCCTTCTCT-TTTTAAAGCCCACACAAATTGGTGGCATCTTTT-AATCCTCAAAAAGCAG
* * *
313601 GACACTTTCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCCCAAAGAGCAGGA
64 GACACCTTCTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCTAGTCCCCAAAGAGCAGGA
313664 CACTTCTTTT
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
152 6 0.06
153 101 0.94
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (153 bp):
AGGACGCCTTCTCTTTTTAAAGCCCACACAAATTGGTGGCATCTTTTAATCCTCAAAAAGCAGGA
CACCTTCTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCTAGTCCCCAAAGAGCAGGATGCC
TTCTCCTTTTAAAGCCAAAGAGT
Found at i:314310 original size:30 final size:30
Alignment explanation
Indices: 314274--314368 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
314264 CATCCTTCTT
314274 TGTATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
*
314304 TGTATCGATACA---T---TTTT---CA-T
1 TGTATCGATACATTTTGGGTTTTACCCAGA
*
314324 TGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATTTTGGGTTTTACCCAGA
*
314354 TGTATCGATATATTT
1 TGTATCGATACATTT
314369 CTCAATGTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
20 12 0.24
21 2 0.04
23 1 0.02
24 4 0.08
26 4 0.08
27 1 0.02
29 2 0.04
30 25 0.49
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (30 bp):
TGTATCGATACATTTTGGGTTTTACCCAGA
Found at i:314331 original size:50 final size:50
Alignment explanation
Indices: 314256--314389 Score: 196
Period size: 50 Copynumber: 2.7 Consensus size: 50
314246 TCACAATTTA
** *
314256 TATCGATACATCCTTCTTTGTATCGATACATTTTGGGTTTTACCCAGATG
1 TATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTACCCAGATG
*
314306 TATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTACCCAGATG
1 TATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTACCCAGATG
* * * *
314356 TATCGATATATTTCTCAATGTCTCGATACATTTT
1 TATCGATACATTTTTCATTGTATCGATACATTTT
314390 AACATTTTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (50 bp):
TATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTACCCAGATG
Found at i:316873 original size:79 final size:79
Alignment explanation
Indices: 316741--316983 Score: 371
Period size: 79 Copynumber: 3.1 Consensus size: 79
316731 TCATTCATGT
* * * * **
316741 TTTTATTTTTAAAACACTGATTTTCCGCAATCAGGGATACTCCAACCTTGTTATTTTCGAAGGGA
1 TTTTATTTTCAAAACACTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGA
316806 TACTCCAACCCCGG
66 TACTCCAACCCCGG
*
316820 TTTTATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGA
1 TTTTATTTTCAAAACACTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGA
316885 TACTCCAACCCCGG
66 TACTCCAACCCCGG
* * *
316899 TTTTATTTTCAAAGCA-TCAATTTTTCACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGG
1 TTTTATTTTCAAAACACT-AATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGG
*
316963 ATACTCCAACCCCGT
65 ATACTCCAACCCCGG
316978 TTTTAT
1 TTTTAT
316984 CTCCAAAATA
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
78 1 0.01
79 150 0.99
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (79 bp):
TTTTATTTTCAAAACACTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAAGGGA
TACTCCAACCCCGG
Found at i:317019 original size:79 final size:77
Alignment explanation
Indices: 316741--317022 Score: 320
Period size: 79 Copynumber: 3.6 Consensus size: 77
316731 TCATTCATGT
* * * **
316741 TTTTATTTTTAAAACACTGATTTTCCGCAATC-AGGGATACTCCAACCTTGTTATTTTCGAAGGG
1 TTTTATTTTCAAAACA-TAATTTTTC-C-ATCGAGGGATACTCCAACCCCGTTATTTTCGAAGGG
316805 ATACTCCAACCCCGG
63 ATACTCCAACCCCGG
316820 TTTTATTTTCAAAACACTAATTTTTCACAATCG-GGGATACTCCAACCCCGTTATTTTCGAAGGG
1 TTTTATTTTCAAAACA-TAATTTTTC-C-ATCGAGGGATACTCCAACCCCGTTATTTTCGAAGGG
316884 ATACTCCAACCCCGG
63 ATACTCCAACCCCGG
* *
316899 TTTTATTTTCAAAGCATCAATTTTTCACCATC-AGGGATACTCCAACCCCGTTATTTTCGAGGGG
1 TTTTATTTTCAAAACAT-AATTTTT--CCATCGAGGGATACTCCAACCCCGTTATTTTCGAAGGG
*
316963 ATACTCCAACCCCGT
63 ATACTCCAACCCCGG
* * * *
316978 TTTTATCTCCAAAATATTAAATTTTT-CATCGAGGGTGTACTCCAA
1 TTTTATTTTCAAAACA-T-AATTTTTCCATCGAGGG-ATACTCCAA
317023 TCGCATACCC
Statistics
Matches: 180, Mismatches: 15, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
77 4 0.02
78 5 0.03
79 161 0.89
80 9 0.05
81 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (77 bp):
TTTTATTTTCAAAACATAATTTTTCCATCGAGGGATACTCCAACCCCGTTATTTTCGAAGGGATA
CTCCAACCCCGG
Found at i:318268 original size:24 final size:24
Alignment explanation
Indices: 318196--318274 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
318186 TATTTTTTCA
*
318196 TTTA-TTTTTAATATAAATAATATT
1 TTTAGTTTTTAATATAAAT-ATAAT
* *
318220 TTAATAGTTATATAAAATAAATATAAT
1 TT--TAGTT-TTTAATATAAATATAAT
318247 TTTAGTTTTTAATATAAATATAAT
1 TTTAGTTTTTAATATAAATATAAT
318271 TTTA
1 TTTA
318275 ATTATTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 21 0.46
25 5 0.11
26 2 0.04
27 8 0.17
28 10 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
TTTAGTTTTTAATATAAATATAAT
Found at i:318285 original size:28 final size:28
Alignment explanation
Indices: 318197--318339 Score: 111
Period size: 28 Copynumber: 5.0 Consensus size: 28
318187 ATTTTTTCAT
318197 TTATT-TTTAATATAAATA-ATATTTTAA
1 TTATTATTTAATATAAATATA-ATTTTAA
* *
318224 -TAGTTATATAAAATAAATATAATTTT-A
1 TTA-TTATTTAATATAAATATAATTTTAA
*
318251 --GTT-TTTAATATAAATATAATTTTAA
1 TTATTATTTAATATAAATATAATTTTAA
*
318276 TTATTATTTAATATAAGTATAATCTTATTTATA
1 TTATTATTTAATATAAATATAA---T-TTTA-A
*
318309 TTTTATTATTTAATATAAATATATTTTTAA
1 --TTATTATTTAATATAAATATAATTTTAA
318339 T
1 T
318340 AATTTTGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
24 18 0.19
25 3 0.03
26 2 0.02
27 5 0.05
28 32 0.34
29 1 0.01
30 1 0.01
31 5 0.05
32 5 0.05
33 1 0.01
35 20 0.22
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (28 bp):
TTATTATTTAATATAAATATAATTTTAA
Found at i:318297 original size:52 final size:51
Alignment explanation
Indices: 318196--318305 Score: 143
Period size: 52 Copynumber: 2.1 Consensus size: 51
318186 TATTTTTTCA
318196 TTTATTTTTAATATAAATAATATTTTAATAGTTATATAAAATAAATATAAT
1 TTTATTTTTAATATAAATAATATTTTAATAGTTATATAAAATAAATATAAT
* * *
318247 TTTAGTTTTTAATATAAAT-ATAATTTTAATTA-TTATTTAATATAAGTATAAT
1 TTTA-TTTTTAATATAAATAAT-ATTTTAA-TAGTTATATAAAATAAATATAAT
*
318299 CTTATTT
1 TTTATTT
318306 ATATTTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
51 9 0.17
52 41 0.79
53 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (51 bp):
TTTATTTTTAATATAAATAATATTTTAATAGTTATATAAAATAAATATAAT
Found at i:318298 original size:22 final size:21
Alignment explanation
Indices: 318263--318306 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
318253 TTTTAATATA
* *
318263 AATATAATTTTAATTATTATTT
1 AATATAAGTATAA-TATTATTT
*
318285 AATATAAGTATAATCTTATTT
1 AATATAAGTATAATATTATTT
318306 A
1 A
318307 TATTTTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATAAGTATAATATTATTT
Found at i:322212 original size:5 final size:5
Alignment explanation
Indices: 322202--322237 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
322192 ATTGAAAAGC
322202 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT C
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT C
322238 TGGTGTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
CCTTT
Found at i:324468 original size:15 final size:15
Alignment explanation
Indices: 324448--324575 Score: 61
Period size: 15 Copynumber: 8.5 Consensus size: 15
324438 AATCATATTT
324448 TTTAAATATATTATA
1 TTTAAATATATTATA
*
324463 TTTAAAATATGTTAATA
1 TTT-AAATATATT-ATA
* *
324480 TATTATATGTAATCTAATA
1 T-TTAAATAT-AT-T-ATA
* *
324499 TTTAAAAATATTGTA
1 TTTAAATATATTATA
*
324514 TTT-GATA-A-TATA
1 TTTAAATATATTATA
*
324526 -TTAAAAATATTAT-
1 TTTAAATATATTATA
* *
324539 TTTAAATATTTTTTAA
1 TTTAAATATATTAT-A
*
324555 TTT-AATATATTATT
1 TTTAAATATATTATA
324569 TTTAAAT
1 TTTAAAT
324576 TCAATATAAT
Statistics
Matches: 82, Mismatches: 19, Indels: 24
0.66 0.15 0.19
Matches are distributed among these distances:
11 2 0.02
12 5 0.06
13 2 0.02
14 18 0.22
15 19 0.23
16 12 0.15
17 10 0.12
18 8 0.10
19 6 0.07
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (15 bp):
TTTAAATATATTATA
Found at i:324503 original size:51 final size:52
Alignment explanation
Indices: 324404--324538 Score: 134
Period size: 51 Copynumber: 2.6 Consensus size: 52
324394 TATATTTTAA
* * *
324404 ATTATAATTTAAAATATTATTAATATATTATGCTAATCATATTTTTTAAATAT
1 ATTAT-ATTTAAAATATTATTAATATATTATGCTAATCATAATATTTAAAAAT
*
324457 ATTATATTTAAAATA-TGTTAATATATTATATG-TAATC-TAATATTTAAAAAT
1 ATTATATTTAAAATATTATTAATATA-T-TATGCTAATCATAATATTTAAAAAT
* * *
324508 ATTGTATTTGATAATA-TATTAAAAATATTAT
1 ATTATATTT-AAAATATTATT-AATATATTAT
324539 TTTAAATATT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
51 31 0.44
52 25 0.36
53 14 0.20
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (52 bp):
ATTATATTTAAAATATTATTAATATATTATGCTAATCATAATATTTAAAAAT
Found at i:324554 original size:51 final size:51
Alignment explanation
Indices: 324404--324554 Score: 130
Period size: 51 Copynumber: 2.9 Consensus size: 51
324394 TATATTTTAA
* *
324404 ATTATAATTTAAAATATTATTAATATA-T-TATGCTAATCATATTTTTTAAATAT
1 ATTAT-ATTTAAAATA-TATTAAAATATTATATG-TAAT-ATATTTTTTAAAAAT
* * * * *
324457 ATTATATTTAAAATATGTTAATATATTATATGTAATCTAATATTTAAAAAT
1 ATTATATTTAAAATATATTAAAATATTATATGTAATATATTTTTTAAAAAT
* * *
324508 ATTGTATTTGATAATATATTAAAAATATTAT-TTTAA-ATATTTTTTAA
1 ATTATATTT-AAAATATATT-AAAATATTATATGTAATATATTTTTTAA
324555 TTTAATATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
51 36 0.44
52 27 0.33
53 18 0.22
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (51 bp):
ATTATATTTAAAATATATTAAAATATTATATGTAATATATTTTTTAAAAAT
Found at i:324570 original size:20 final size:20
Alignment explanation
Indices: 324545--324583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
324535 TTATTTTAAA
* *
324545 TATTTTTTAATTTAATATAT
1 TATTTTTAAATTCAATATAT
324565 TATTTTTAAATTCAATATA
1 TATTTTTAAATTCAATATA
324584 ATAATCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTTAAATTCAATATAT
Found at i:326142 original size:16 final size:16
Alignment explanation
Indices: 326118--326189 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
326108 TTTATTATAA
*
326118 TTATTTTTA-AAATATT
1 TTATATTTATAAATA-T
326134 TTATATTTATATAA-AT
1 TTATATTTATA-AATAT
326150 TTATATTATATAAAT-T
1 TTATATT-TATAAATAT
*
326166 TTATTATATT-TATATAT
1 TTA-TAT-TTATAAATAT
326183 TTATATT
1 TTATATT
326190 ATATTATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
15 1 0.02
16 29 0.62
17 14 0.30
18 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTATAAATAT
Found at i:326172 original size:14 final size:15
Alignment explanation
Indices: 326133--326193 Score: 70
Period size: 15 Copynumber: 3.8 Consensus size: 15
326123 TTTAAAATAT
326133 TTTATATTTATATAAA
1 TTTATA-TTATATAAA
326149 TTTATATTATATAAA
1 TTTATATTATATAAA
326164 TTT-TATTATATTTATATA
1 TTTATATTATA--TA-A-A
326182 TTTATATTATAT
1 TTTATATTATAT
326194 TATAATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.17
15 12 0.30
16 8 0.20
17 2 0.05
18 4 0.10
19 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:326174 original size:19 final size:20
Alignment explanation
Indices: 326150--326197 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
326140 TTATATAAAT
326150 TTATATTATATAAATTT-TA
1 TTATATTATATAAATTTATA
*
326169 TTATATT-TATATATTTATA
1 TTATATTATATAAATTTATA
326188 TTATATTATA
1 TTATATTATA
326198 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.31
19 16 0.62
20 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATTATATAAATTTATA
Found at i:326190 original size:33 final size:33
Alignment explanation
Indices: 326100--326193 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
326090 CGTTTTTATG
* *
326100 TTTATTAT-TTTATTATAATTAT-TTTTA-AAAT
1 TTTATTATATTTA-TATATTTATATTATATAAAT
*
326131 ATT-TTATATTTATATAAATTTATATTATATAAAT
1 TTTATTATATTTATAT--ATTTATATTATATAAAT
326165 TTTATTATATTTATATATTTATATTATAT
1 TTTATTATATTTATATATTTATATTATAT
326194 TATAATTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
30 7 0.13
31 6 0.11
32 5 0.09
33 17 0.32
34 6 0.11
35 12 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTATTATATTTATATATTTATATTATATAAAT
Found at i:326471 original size:18 final size:18
Alignment explanation
Indices: 326434--326492 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
326424 TTATATTGTG
* *
326434 TTATATAAAAATATTATAT
1 TTATATAAAATTAAT-TAT
326453 TTATATAAAATTAATTAT
1 TTATATAAAATTAATTAT
* *
326471 TTA-ATTAAATTTAATAAT
1 TTATA-TAAAATTAATTAT
326489 TTAT
1 TTAT
326493 GTATGTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 20 0.59
19 13 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATAAAATTAATTAT
Found at i:326598 original size:9 final size:9
Alignment explanation
Indices: 326553--326620 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
326543 ATATAAATTA
*
326553 TTAAATATG
1 TTAAATATT
326562 TTAAA-ATT
1 TTAAATATT
326570 TTAAATA--
1 TTAAATATT
*
326577 -TAAAAATT
1 TTAAATATT
*
326585 ATAAATATT
1 TTAAATATT
*
326594 TTAAATATA
1 TTAAATATT
*
326603 TTAATTATAT
1 TTAAATAT-T
326613 TTAAATAT
1 TTAAATAT
326621 ATAATATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
6 5 0.11
8 7 0.15
9 27 0.59
10 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (9 bp):
TTAAATATT
Found at i:326599 original size:24 final size:23
Alignment explanation
Indices: 326563--326611 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
326553 TTAAATATGT
326563 TAAAATTTTAAATATAAAAATTA
1 TAAAATTTTAAATATAAAAATTA
**
326586 TAAATATTTTAAATATATTAATTA
1 TAAA-ATTTTAAATATAAAAATTA
326610 TA
1 TA
326612 TTTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAATTTTAAATATAAAAATTA
Found at i:326612 original size:20 final size:21
Alignment explanation
Indices: 326589--326647 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
326579 AAAATTATAA
326589 ATATTTTAAATATATTA-ATT
1 ATATTTTAAATATATTATATT
*
326609 ATA-TTTAAATATATAATATT
1 ATATTTTAAATATATTATATT
* *
326629 ATATAATTAAACATATTAT
1 ATAT-TTTAAATATATTAT
326648 TTTTTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.38
20 9 0.28
22 11 0.34
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTTTAAATATATTATATT
Found at i:326639 original size:22 final size:19
Alignment explanation
Indices: 326580--326632 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
326570 TTAAATATAA
326580 AAAT-TATAAA-TAT-TTT
1 AAATATATAAATTATATTT
*
326596 AAATATATTAATTATATTT
1 AAATATATAAATTATATTT
326615 AAATATATAATATTATAT
1 AAATATATAA-ATTATAT
326633 AATTAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 3 0.10
19 12 0.39
20 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATATAAATTATATTT
Found at i:326655 original size:22 final size:22
Alignment explanation
Indices: 326607--326655 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
326597 AATATATTAA
* *
326607 TTATATTTAAATATATAATATT
1 TTATAATTAAACATATAATATT
* * *
326629 ATATAATTAAACATATTATTTT
1 TTATAATTAAACATATAATATT
326651 TTATA
1 TTATA
326656 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATAATTAAACATATAATATT
Found at i:327503 original size:2 final size:2
Alignment explanation
Indices: 327496--327530 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
327486 AACAAAAACA
327496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
327531 AAATATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:328044 original size:13 final size:13
Alignment explanation
Indices: 328026--328050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328016 AAAAAATATA
328026 AATTTTTTATTTG
1 AATTTTTTATTTG
328039 AATTTTTTATTT
1 AATTTTTTATTT
328051 TATAATGACG
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
AATTTTTTATTTG
Found at i:333005 original size:33 final size:34
Alignment explanation
Indices: 332931--333018 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 34
332921 TAAAATTATT
*
332931 ATTTAATAATAAAAA-TATA-TTT--T-ATTTAA
1 ATTTAATCATAAAAATTATATTTTAATAATTTAA
332960 ATTTAATCATAAAAATTATATTTTAATAATTTAA
1 ATTTAATCATAAAAATTATATTTTAATAATTTAA
*
332994 A-TTAATTATAAAAATTATATTTTAA
1 ATTTAATCATAAAAATTATATTTTAA
333019 AAATATAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.27
30 4 0.08
31 3 0.06
33 24 0.46
34 7 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (34 bp):
ATTTAATCATAAAAATTATATTTTAATAATTTAA
Found at i:339284 original size:27 final size:25
Alignment explanation
Indices: 339252--339301 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
339242 AAATATATTT
*
339252 TCTTTTCATTTTTTTCACTCTTATACA
1 TCTTTTCACTTTTTT-ACT-TTATACA
339279 TCTTTTCACTTTTTTACTTTATA
1 TCTTTTCACTTTTTTACTTTATA
339302 AAGTATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 3 0.14
27 14 0.64
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (25 bp):
TCTTTTCACTTTTTTACTTTATACA
Done.