Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold168
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1096678
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.29
Warning! 140106 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:567240 original size:30 final size:29
Alignment explanation
Indices: 567200--567279 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
567190 AGGTCGAAGA
567200 TGCGAGAGTGCGAAGTTGCGAA-G-GCGAAAG
1 TGCGA-AGTGCGAAG--GCGAAGGAGCGAAAG
*
567230 TGCGATAGTGCGACGGCGAAGGAGCGAAAG
1 TGCGA-AGTGCGAAGGCGAAGGAGCGAAAG
*
567260 TGCGAAGATGCGATGGCGAA
1 TGCGAAG-TGCGAAGGCGAA
567280 AGTGCGAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.11
29 3 0.07
30 36 0.82
ACGTcount: A:0.30, C:0.15, G:0.42, T:0.12
Consensus pattern (29 bp):
TGCGAAGTGCGAAGGCGAAGGAGCGAAAG
Found at i:567287 original size:30 final size:29
Alignment explanation
Indices: 567223--567294 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
567213 AGTTGCGAAG
*
567223 GCGAAAGTGCGATAGTGCGACGGCGAAGGA
1 GCGAAAGTGCGA-AGTGCGACGGCGAAAGA
* *
567253 GCGAAAGTGCGAAGATGCGATGGCGAAAGT
1 GCGAAAGTGCGAAG-TGCGACGGCGAAAGA
567283 GCG-AAG-GCGAAG
1 GCGAAAGTGCGAAG
567295 GAGCGATACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.16
29 5 0.13
30 27 0.71
ACGTcount: A:0.32, C:0.15, G:0.43, T:0.10
Consensus pattern (29 bp):
GCGAAAGTGCGAAGTGCGACGGCGAAAGA
Found at i:567300 original size:14 final size:14
Alignment explanation
Indices: 567239--567300 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
567229 GTGCGATAGT
*
567239 GCGACGGCGAAGGA
1 GCGAAGGCGAAGGA
567253 GCGAAAGTGCGAA-GA
1 GCG-AAG-GCGAAGGA
* * *
567268 TGCGATGGCGAAAGT
1 -GCGAAGGCGAAGGA
567283 GCGAAGGCGAAGGA
1 GCGAAGGCGAAGGA
567297 GCGA
1 GCGA
567301 TACTACTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
14 23 0.61
15 7 0.18
16 8 0.21
ACGTcount: A:0.32, C:0.16, G:0.45, T:0.06
Consensus pattern (14 bp):
GCGAAGGCGAAGGA
Found at i:567300 original size:22 final size:22
Alignment explanation
Indices: 567216--567300 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
567206 AGTGCGAAGT
* * *
567216 TGCGAAGGCGAAAGTGCGATAG
1 TGCGAAGGCGAAGGAGCGAAAG
*
567238 TGCGACGGCGAAGGAGCGAAAG
1 TGCGAAGGCGAAGGAGCGAAAG
*
567260 TGCGAAGATGCG-ATG-GCGAAAG
1 TGCGAAG--GCGAAGGAGCGAAAG
567282 TGCGAAGGCGAAGGAGCGA
1 TGCGAAGGCGAAGGAGCGA
567301 TACTACTATC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
22 42 0.81
23 2 0.04
24 3 0.06
ACGTcount: A:0.32, C:0.15, G:0.44, T:0.09
Consensus pattern (22 bp):
TGCGAAGGCGAAGGAGCGAAAG
Found at i:567332 original size:14 final size:14
Alignment explanation
Indices: 567315--567370 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
567305 ACTATCGCTC
567315 CTTCGC-CTTCGCAA
1 CTTCGCACTTCGC-A
567329 CTTCGCACTCTCGCA
1 CTTCGCACT-TCGCA
567344 -TTCGCAACTTCGCA
1 CTTCGC-ACTTCGCA
567358 CTTTCGC-CTTCGC
1 C-TTCGCACTTCGC
567371 CTTTTTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 22 0.59
15 6 0.16
16 9 0.24
ACGTcount: A:0.12, C:0.43, G:0.14, T:0.30
Consensus pattern (14 bp):
CTTCGCACTTCGCA
Found at i:567342 original size:22 final size:22
Alignment explanation
Indices: 567317--567370 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
567307 TATCGCTCCT
567317 TCGCCTTCGCAACTTCGCACTC
1 TCGCCTTCGCAACTTCGCACTC
* *
567339 TCGCATTCGCAACTTCGCACTT
1 TCGCCTTCGCAACTTCGCACTC
567361 TCGCCTTCGC
1 TCGCCTTCGC
567371 CTTTTTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.13, C:0.43, G:0.15, T:0.30
Consensus pattern (22 bp):
TCGCCTTCGCAACTTCGCACTC
Found at i:567363 original size:8 final size:7
Alignment explanation
Indices: 567315--567370 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
567305 ACTATCGCTC
567315 CTTCGC-
1 CTTCGCA
567321 CTTCGCAA
1 CTTCGC-A
567329 CTTCGCA
1 CTTCGCA
567336 CTCTCGCA
1 CT-TCGCA
567344 -TTCGCAA
1 CTTCGC-A
567351 CTTCGCA
1 CTTCGCA
567358 CTTTCGC-
1 C-TTCGCA
567365 CTTCGC
1 CTTCGC
567371 CTTTTTTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 15 0.34
7 8 0.18
8 21 0.48
ACGTcount: A:0.12, C:0.43, G:0.14, T:0.30
Consensus pattern (7 bp):
CTTCGCA
Found at i:568070 original size:22 final size:22
Alignment explanation
Indices: 568042--568103 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
568032 TTAAAAAAAG
568042 GCGAAGGCGAAAGTGCGAAGAT
1 GCGAAGGCGAAAGTGCGAAGAT
* *
568064 GCGAAGGCGAGAGTGCGAAGTT
1 GCGAAGGCGAAAGTGCGAAGAT
* *
568086 GCGATGGCGAAGGTGCGA
1 GCGAAGGCGAAAGTGCGA
568104 TAGTAGTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.45, T:0.11
Consensus pattern (22 bp):
GCGAAGGCGAAAGTGCGAAGAT
Found at i:568135 original size:8 final size:7
Alignment explanation
Indices: 568118--568235 Score: 68
Period size: 8 Copynumber: 16.3 Consensus size: 7
568108 AGTATCGCTT
568118 CTTCGC-
1 CTTCGCA
568124 CTTCGCAA
1 CTTCGC-A
568132 CTTCGCA
1 CTTCGCA
568139 CTTTCGC-
1 C-TTCGCA
568146 CTTCGCA
1 CTTCGCA
*
568153 TCTTCGCG
1 -CTTCGCA
*
568161 CTT-G-G
1 CTTCGCA
568166 CTGTCGCA
1 CT-TCGCA
568174 TCTTCGCA
1 -CTTCGCA
*
568182 CTTTCGCTC
1 C-TTCGC-A
568191 CTTCGC-
1 CTTCGCA
*
568197 CGTCGCA
1 CTTCGCA
568204 CCTTCGCA
1 -CTTCGCA
568212 CTTTCGC-
1 C-TTCGCA
568219 CTTCGCAA
1 CTTCGC-A
568227 CTTCGCA
1 CTTCGCA
568234 CT
1 CT
568236 CTCACACCTC
Statistics
Matches: 91, Mismatches: 5, Indels: 31
0.72 0.04 0.24
Matches are distributed among these distances:
5 3 0.03
6 23 0.25
7 13 0.14
8 49 0.54
9 3 0.03
ACGTcount: A:0.09, C:0.42, G:0.17, T:0.32
Consensus pattern (7 bp):
CTTCGCA
Found at i:568144 original size:22 final size:22
Alignment explanation
Indices: 568119--568188 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
568109 GTATCGCTTC
*
568119 TTCGCCTTCGCAACTTCGCACT
1 TTCGCCTTCGCATCTTCGCACT
*
568141 TTCGCCTTCGCATCTTCGCGC-
1 TTCGCCTTCGCATCTTCGCACT
*
568162 TT-GGCTGTCGCATCTTCGCACT
1 TTCGCCT-TCGCATCTTCGCACT
568184 TTCGC
1 TTCGC
568189 TCCTTCGCCG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.08
21 15 0.38
22 21 0.52
23 1 0.03
ACGTcount: A:0.09, C:0.39, G:0.19, T:0.34
Consensus pattern (22 bp):
TTCGCCTTCGCATCTTCGCACT
Found at i:568202 original size:22 final size:22
Alignment explanation
Indices: 568177--568234 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
568167 TGTCGCATCT
* *
568177 TCGCACTTTCGCTCCTTCGCCG
1 TCGCACCTTCGCACCTTCGCCG
* *
568199 TCGCACCTTCGCACTTTCGCCT
1 TCGCACCTTCGCACCTTCGCCG
*
568221 TCGCAACTTCGCAC
1 TCGCACCTTCGCAC
568235 TCTCACACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.10, C:0.45, G:0.16, T:0.29
Consensus pattern (22 bp):
TCGCACCTTCGCACCTTCGCCG
Found at i:568232 original size:14 final size:14
Alignment explanation
Indices: 568132--568225 Score: 54
Period size: 14 Copynumber: 6.5 Consensus size: 14
568122 GCCTTCGCAA
568132 CTTCGCACTTTCGC
1 CTTCGCACTTTCGC
568146 CTTCGCA-TCTTCGC
1 CTTCGCACT-TTCGC
* *
568160 GCTT-G-GCTGTCGC
1 -CTTCGCACTTTCGC
568173 ATCTTCGCACTTTCGCTC
1 --CTTCGCACTTTCG--C
*
568191 CTTCGC-C-GTCGCAC
1 CTTCGCACTTTCG--C
568205 CTTCGCACTTTCGC
1 CTTCGCACTTTCGC
568219 CTTCGCA
1 CTTCGCA
568226 ACTTCGCACT
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
13 5 0.08
14 36 0.58
15 6 0.10
16 14 0.23
18 1 0.02
ACGTcount: A:0.07, C:0.41, G:0.18, T:0.33
Consensus pattern (14 bp):
CTTCGCACTTTCGC
Found at i:568234 original size:30 final size:29
Alignment explanation
Indices: 568145--568224 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 29
568135 CGCACTTTCG
* * *
568145 CCTTCGCA-TCTTCGCGCTTGGCTGTCGCA
1 CCTTCGCACT-TTCGCCCTTCGCCGTCGCA
*
568174 TCTTCGCACTTTCGCTCCTTCGCCGTCGCA
1 CCTTCGCACTTTCGC-CCTTCGCCGTCGCA
568204 CCTTCGCACTTTCG-CCTTCGC
1 CCTTCGCACTTTCGCCCTTCGC
568225 AACTTCGCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.16
29 12 0.27
30 25 0.57
ACGTcount: A:0.06, C:0.42, G:0.19, T:0.33
Consensus pattern (29 bp):
CCTTCGCACTTTCGCCCTTCGCCGTCGCA
Found at i:569001 original size:21 final size:21
Alignment explanation
Indices: 568975--569068 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
568965 ATGGTTATTT
*
568975 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTCAACATAAATA
**
568996 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAATA
*
569017 TCTGACAAGTCAACAT-TATCA
1 TCTGACAAGTCAACATAAAT-A
* * * *
569038 TATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAATA
569059 TCTGACAAGT
1 TCTGACAAGT
569069 GGTGGCAGAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.95
22 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (21 bp):
TCTGACAAGTCAACATAAATA
Found at i:569048 original size:42 final size:42
Alignment explanation
Indices: 568975--569068 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
568965 ATGGTTATTT
* * *
568975 TCTGACAAGTCAACATAAAGATCTGACAAGTTGACATAAATA
1 TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
* * * *
569017 TCTGACAAGTCAACATTATCATATGAGAAGTTAACATAATTA
1 TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
569059 TCTGACAAGT
1 TCTGACAAGT
569069 GGTGGCAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (42 bp):
TCTGACAAGTCAACATAAACATATGACAAGTTAACATAAATA
Found at i:573977 original size:70 final size:69
Alignment explanation
Indices: 573879--574081 Score: 257
Period size: 70 Copynumber: 2.9 Consensus size: 69
573869 AGATAACTGC
* * * *
573879 TTGCATGGGCTAGTTAGAAGAACTGATATCACTTTAA-ACGGACAACTAGTTAGTTAGTGGAAAT
1 TTGCATGGGCTAGTAAAAAGAACTGATATCAC-GTAATACGGGCAAC-AGTTAGTTAGTGGAAAT
573943 AATTGA
64 AATTGA
* ** * *
573949 TTGCATGGGCTAGTAAAAAGAACTGATATCACGTAATTCGGGGTACAGGTTAGTTAGTTGAAATT
1 TTGCATGGGCTAGTAAAAAGAACTGATATCACGTAATACGGGCAACA-GTTAGTTAGTGGAAATA
574014 ATTGA
65 ATTGA
* *
574019 TTGCATGGGCTAATAAAAA-AACTGATATCACGTAATACGGGCAACAAATTAGTTAGTGGAAAT
1 TTGCATGGGCTAGTAAAAAGAACTGATATCACGTAATACGGGCAAC-AGTTAGTTAGTGGAAAT
574082 TATGATAATT
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
69 41 0.36
70 74 0.64
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (69 bp):
TTGCATGGGCTAGTAAAAAGAACTGATATCACGTAATACGGGCAACAGTTAGTTAGTGGAAATAA
TTGA
Found at i:584652 original size:23 final size:23
Alignment explanation
Indices: 584626--584698 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
584616 CTGAATCACA
584626 CCGGAAACAGTTATATTGCCCTC
1 CCGGAAACAGTTATATTGCCCTC
584649 CCGGAAACAGTTATATT----TC
1 CCGGAAACAGTTATATTGCCCTC
* *
584668 ACAGGAAATAGTTATATTGCCCTC
1 -CCGGAAACAGTTATATTGCCCTC
584692 CC-GAAAC
1 CCGGAAAC
584699 TGTAATATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.05
20 15 0.37
22 4 0.10
23 18 0.44
24 2 0.05
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
CCGGAAACAGTTATATTGCCCTC
Found at i:589615 original size:11 final size:11
Alignment explanation
Indices: 589601--589639 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
589591 CAAAATGTAA
589601 ACAAAAACATG
1 ACAAAAACATG
589612 ACAAAAAGCATG
1 ACAAAAA-CATG
* *
589624 ACAATAACATA
1 ACAAAAACATG
589635 ACAAA
1 ACAAA
589640 GAGCTCTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.64, C:0.18, G:0.08, T:0.10
Consensus pattern (11 bp):
ACAAAAACATG
Found at i:593072 original size:2 final size:2
Alignment explanation
Indices: 593065--593140 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
593055 ATGCATACTG
593065 CT CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
593106 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
593141 GTAGAAAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:629332 original size:4 final size:4
Alignment explanation
Indices: 629295--629325 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
629285 TGAAAAGTTT
*
629295 ACGG ACAG ACGG ACGG ACGG ACGG ACGG ACG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACG
629326 ACAGACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.26, G:0.45, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:630751 original size:276 final size:277
Alignment explanation
Indices: 630205--630767 Score: 891
Period size: 276 Copynumber: 2.0 Consensus size: 277
630195 TACATGTAAA
** *
630205 TACCGTATTTTTCGGAAATTGGGTCGATACTTTTTTCCCTGACACGTGGACCTCGCCCTATTCAT
1 TACCGTATTTCACGGAAATTAGGTCGATACTTTTTTCCCTGACACGTGGACCTCGCCCTATTCAT
630270 AGCTTCGCCCAATTTATGTTTTTTTTTTTTTACTTGGAAAATTTGATATGAAATTTTGCAAAAAT
66 AGCTTCGCCCAATTTATGTTTTTTTTTTTTTA-TTGG---A-TTG--A-GAAATTTTGCAAAAAT
**
630335 TTATGCAACCCTCCAATAAAATTGTGAGTGTTTACTATAATACTGCTTGAATTTCTGTGTAAAAA
123 TTATGCAACCCTCCAATAAAATCATGAGTGTTTACTATAATACTGCTTGAATTTCTGTGTAAAAA
*
630400 TCGTATGGATTTTAATCAATATACTGTAGTAATTTATCATTTATACAAAATTAAATGTAAATAGA
188 TCGTATGGATTTTAATCAATATACTGTAGTAATTTATCATTTAAACAAAATTAAATGTAAATAGA
*
630465 TTTGTTTCTTCTTACATTTCTTACT
253 TTTATTTCTTCTTACATTTCTTACT
* **
630490 TACCGTATTTCACGGAATTTAGGTCGATACTTTTTTCCCCTGACATTTGGACCTCGCCCTATTCA
1 TACCGTATTTCACGGAAATTAGGTCGATACTTTTTT-CCCTGACACGTGGACCTCGCCCTATTCA
*
630555 TCGCTTCGCCCAATTTATGATTTTTCTTTTTTTT-TTGG-TTG-G-AATTTTGCAAAAATTTATG
65 TAGCTTCGCCCAATTTATG-TTTTT-TTTTTTTTATTGGATTGAGAAATTTTGCAAAAATTTATG
630616 CAACCCTCCAATAAAATCATGAGTGTTTACTATAATACTGCTTGAATTTCTGTGTAAAAATCGTA
128 CAACCCTCCAATAAAATCATGAGTGTTTACTATAATACTGCTTGAATTTCTGTGTAAAAATCGTA
*
630681 TGGATTTTAATCAATATACTGTAGTAATTTATCATTTAAACAAAATTGAATGTAAATAGATTTAT
193 TGGATTTTAATCAATATACTGTAGTAATTTATCATTTAAACAAAATTAAATGTAAATAGATTTAT
630746 TTCTTCTTACATTTCTTACT
258 TTCTTCTTACATTTCTTACT
630766 TA
1 TA
630768 GATCACTGAC
Statistics
Matches: 263, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
276 166 0.63
277 1 0.00
281 3 0.01
285 32 0.12
286 48 0.18
287 5 0.02
288 8 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (277 bp):
TACCGTATTTCACGGAAATTAGGTCGATACTTTTTTCCCTGACACGTGGACCTCGCCCTATTCAT
AGCTTCGCCCAATTTATGTTTTTTTTTTTTTATTGGATTGAGAAATTTTGCAAAAATTTATGCAA
CCCTCCAATAAAATCATGAGTGTTTACTATAATACTGCTTGAATTTCTGTGTAAAAATCGTATGG
ATTTTAATCAATATACTGTAGTAATTTATCATTTAAACAAAATTAAATGTAAATAGATTTATTTC
TTCTTACATTTCTTACT
Found at i:670199 original size:15 final size:15
Alignment explanation
Indices: 670164--670234 Score: 54
Period size: 16 Copynumber: 4.6 Consensus size: 15
670154 GCCCTTGACG
* *
670164 CCGTTCGCTCTAGTTT
1 CCGTTCGCCCTAG-GT
670180 CCGTTCGCCCTAGGT
1 CCGTTCGCCCTAGGT
* *
670195 CCGTTCGCTCTTGACG-
1 CCGTTCGC-CCT-AGGT
* *
670211 CCGTTCGCACTGGGT
1 CCGTTCGCCCTAGGT
670226 CCGTTCGCC
1 CCGTTCGCC
670235 TTATTTTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.02
15 18 0.42
16 22 0.51
17 2 0.05
ACGTcount: A:0.06, C:0.38, G:0.25, T:0.31
Consensus pattern (15 bp):
CCGTTCGCCCTAGGT
Found at i:670202 original size:31 final size:31
Alignment explanation
Indices: 670164--670233 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
670154 GCCCTTGACG
*** *
670164 CCGTTCGCTCTAGTTTCCGTTCGCCCTAGGT
1 CCGTTCGCTCTAGACGCCGTTCGCACTAGGT
* *
670195 CCGTTCGCTCTTGACGCCGTTCGCACTGGGT
1 CCGTTCGCTCTAGACGCCGTTCGCACTAGGT
670226 CCGTTCGC
1 CCGTTCGC
670234 CTTATTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.06, C:0.37, G:0.26, T:0.31
Consensus pattern (31 bp):
CCGTTCGCTCTAGACGCCGTTCGCACTAGGT
Found at i:671980 original size:14 final size:15
Alignment explanation
Indices: 671943--671980 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
671933 AACGATAATC
*
671943 AGAGCGAACGGACTT
1 AGAGCGAACGGACTA
671958 AGAGCGAACGGACTA
1 AGAGCGAACGGACTA
671973 AG-GCGAAC
1 AGAGCGAAC
671981 AGGTGGATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.37, C:0.21, G:0.34, T:0.08
Consensus pattern (15 bp):
AGAGCGAACGGACTA
Found at i:674600 original size:17 final size:16
Alignment explanation
Indices: 674573--674607 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
674563 ACGGCACAAT
674573 GTACTGGCGAGAAATG
1 GTACTGGCGAGAAATG
*
674589 GTACTCGGCGAGAACTG
1 GTACT-GGCGAGAAATG
674606 GT
1 GT
674608 CGCACGCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (16 bp):
GTACTGGCGAGAAATG
Found at i:675141 original size:17 final size:17
Alignment explanation
Indices: 675119--675151 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
675109 CTGTGGGAAC
675119 TGTATAATGACCTGATA
1 TGTATAATGACCTGATA
*
675136 TGTATAATGTCCTGAT
1 TGTATAATGACCTGAT
675152 GACCTGATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (17 bp):
TGTATAATGACCTGATA
Found at i:675679 original size:2 final size:2
Alignment explanation
Indices: 675672--675732 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
675662 TTAAGACTGT
675672 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
675714 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
675733 GAAACAGCTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:676991 original size:17 final size:17
Alignment explanation
Indices: 676969--677001 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
676959 CCATCAGGTC
676969 ATCAGGACATTATACAT
1 ATCAGGACATTATACAT
*
676986 ATCAGGTCATTATACA
1 ATCAGGACATTATACA
677002 GTCCCAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (17 bp):
ATCAGGACATTATACAT
Found at i:690736 original size:19 final size:19
Alignment explanation
Indices: 690712--690750 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
690702 CTTGACTACC
*
690712 TCTGTAAATGTATTTCTTG
1 TCTGTAAATCTATTTCTTG
*
690731 TCTGTAAATCTATTTTTTG
1 TCTGTAAATCTATTTCTTG
690750 T
1 T
690751 GAGGCATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (19 bp):
TCTGTAAATCTATTTCTTG
Found at i:701147 original size:166 final size:166
Alignment explanation
Indices: 700868--701712 Score: 1195
Period size: 166 Copynumber: 5.2 Consensus size: 166
700858 TATAGGGTGC
700868 ATGTCTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCT
1 ATGT-TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCT
700933 TGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAG
65 TGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAG
700998 GCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
130 GCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
*
701035 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAACTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
701100 GTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGG
66 GTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGG
*
701165 CGAGGTTCAAAGTTTAACATAGAAATACATAGG-AA
131 CGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
* *
701200 ATTTTTTAAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACATAAGCT
1 ATGTTTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCT
* *
701265 TGTATACATAGCGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAG
65 TGTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAG
* *
701330 GCGGGGTTCAAA-TTTAACATAGATATACCTTAGGAAA
130 GCGGGGTTCAAAGTTTAACATAGAAATA-CATAGGAAA
*
701367 ATGTTTAAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
* * * ** * **
701432 GTATGTATAATGAAGATTCTAAATTGTAGAAATCGTGACCCTCAAATCAAAACTGCAGCCCCAGG
66 GTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGG
* * *
701497 CGGGGTTCAAAGTTTATCATAGAACTACATATGAAAA
131 CGGGGTTCAAAGTTTAACATAGAAATACATA-GGAAA
* * * * ** * *
701534 ATG-TTTAAAAATTTTCTTCTCAAAAACCACTTCACCAAAAATGCCAATACATACACAAACGGTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
* * *
701598 GTATATATAGTGAAG-------ATTGTAAAAATCGTGACCC-CTGAACAAAAAGTGGGGCCCCAG
66 GTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTC-GGACCAAAACTGGGGCCCCAG
** * * *
701655 TAGGGGTTTAGATTTTAACAT----AT--ATAGGAAA
130 GCGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
701686 ATGTTTT-AAAATCTTCTTCTCAAGAAC
1 ATGTTTTAAAAATCTTCTTCTCAAGAAC
701713 TATAGTGCAA
Statistics
Matches: 615, Mismatches: 56, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
152 25 0.04
153 6 0.01
155 1 0.00
158 1 0.00
159 48 0.08
165 22 0.04
166 482 0.78
167 30 0.05
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (166 bp):
ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTT
GTATATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGG
CGGGGTTCAAAGTTTAACATAGAAATACATAGGAAA
Found at i:702430 original size:165 final size:165
Alignment explanation
Indices: 702180--702587 Score: 473
Period size: 165 Copynumber: 2.5 Consensus size: 165
702170 CGGTATATAT
* * * * *
702180 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAGTTTGTCAGATAACTACGTA
1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCA
* * * *
702244 AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCTGT-GACCTCAATCTAATACTGGGGC
65 AGCATCCTCAAATAATGTAGATTCCAAATAATTAAAA-CTGTAGACCTCAA-CTAATACTGGGGC
* * * *
702307 CCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG
128 CCCAAGAGGGGTTCAAAGTTTAACATAGAAAGATAAAG
* * * *
702345 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTATGCAA
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA
* * * ** *
702410 GCATCCTTAAATAATGTAGATTCCAAATAATTAAAACTTTAGCCCTGGACTAATACTGTGGCCCC
66 GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACTGTAGACCTCAACTAATACTGGGGCCCC
*
702475 AAGAGGGGTTCAAAGTTTAACATAGAAAGATAAAT
131 AAGAGGGGTTCAAAGTTTAACATAGAAAGATAAAG
* * * * *
702510 TGAAAATGTTTTTAAAAA-GTTTTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTATTATGC
1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGC
*
702574 AAGGATCCTCAAAT
64 AAGCATCCTCAAAT
702588 TGTGTAAACT
Statistics
Matches: 203, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
164 3 0.01
165 132 0.65
166 61 0.30
167 7 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (165 bp):
GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA
GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACTGTAGACCTCAACTAATACTGGGGCCCC
AAGAGGGGTTCAAAGTTTAACATAGAAAGATAAAG
Found at i:706257 original size:15 final size:16
Alignment explanation
Indices: 706224--706258 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
706214 ATTAAAAAAA
706224 ATTTATAATATAGAAT
1 ATTTATAATATAGAAT
*
706240 ATTTATTATATA-AAT
1 ATTTATAATATAGAAT
706255 ATTT
1 ATTT
706259 TTTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTATAATATAGAAT
Found at i:706692 original size:25 final size:24
Alignment explanation
Indices: 706658--706705 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
706648 NNNNNNNNNA
706658 AAAAAATTTATAATATAGAATATTC
1 AAAAAATTTATAATATA-AATATTC
* *
706683 AAAATATTTATTATATAAATATT
1 AAAAAATTTATAATATAAATATT
706706 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAAAATTTATAATATAAATATTC
Found at i:716380 original size:2 final size:2
Alignment explanation
Indices: 716373--716402 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
716363 TTTGTTATTC
*
716373 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
716403 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:717132 original size:27 final size:27
Alignment explanation
Indices: 717094--717150 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
717084 TTAATAAATA
717094 AGGGTGATAAAGTCTATATCCTTTTGT
1 AGGGTGATAAAGTCTATATCCTTTTGT
717121 AGGGTGATAAAGTCTATATCCTTTTGT
1 AGGGTGATAAAGTCTATATCCTTTTGT
717148 AGG
1 AGG
717151 TATATGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.39
Consensus pattern (27 bp):
AGGGTGATAAAGTCTATATCCTTTTGT
Found at i:717300 original size:23 final size:23
Alignment explanation
Indices: 717267--717312 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
717257 TCCATTTACA
*
717267 CAGTACTTTGTT-TCTAGTACATG
1 CAGTACCTTGTTCT-TAGTACATG
717290 CAGTACCTTGTTCTTAGTACATG
1 CAGTACCTTGTTCTTAGTACATG
717313 TACTCGCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (23 bp):
CAGTACCTTGTTCTTAGTACATG
Found at i:717835 original size:18 final size:18
Alignment explanation
Indices: 717814--717855 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
717804 TTGTAGGGAA
*
717814 AAATATGAACAAATGCAC
1 AAATATGAACAAATGAAC
*
717832 AAATATGAACAGATGAAC
1 AAATATGAACAAATGAAC
717850 AAATAT
1 AAATAT
717856 TTGTATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (18 bp):
AAATATGAACAAATGAAC
Found at i:720189 original size:2 final size:2
Alignment explanation
Indices: 720182--720222 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
720172 AATGACAGCA
720182 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
720223 GGGGCACTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:723200 original size:14 final size:14
Alignment explanation
Indices: 723181--723209 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
723171 AATAGAGGTA
723181 ATATATGTATTGGT
1 ATATATGTATTGGT
723195 ATATATGTATTGGT
1 ATATATGTATTGGT
723209 A
1 A
723210 ACACTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATATATGTATTGGT
Found at i:733434 original size:12 final size:14
Alignment explanation
Indices: 733407--733444 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
733397 GAAAATATAC
733407 ATAATATATGTAAT
1 ATAATATATGTAAT
733421 ATAATATAT-T-AT
1 ATAATATATGTAAT
733433 ATAATAATATGT
1 ATAAT-ATATGT
733445 CAAGACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 5 0.23
14 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
ATAATATATGTAAT
Found at i:740878 original size:2 final size:2
Alignment explanation
Indices: 740871--740902 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
740861 CAAAAGAGAA
740871 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
740903 AATATCTGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:742247 original size:2 final size:2
Alignment explanation
Indices: 742235--742270 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
742225 GAAAGGAATA
*
742235 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
742271 GTTAAATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:742854 original size:2 final size:2
Alignment explanation
Indices: 742847--742916 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
742837 ATGAAAACAA
742847 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
742889 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
742917 ATAAGCAACA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:747081 original size:21 final size:21
Alignment explanation
Indices: 747055--747097 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
747045 CCACCCATAT
*
747055 TGTTTTGCCCTTGTCTATTCA
1 TGTTTTGCCCTGGTCTATTCA
*
747076 TGTTTTGCCCTGGTCTGTTCA
1 TGTTTTGCCCTGGTCTATTCA
747097 T
1 T
747098 TGTGTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.23, G:0.19, T:0.51
Consensus pattern (21 bp):
TGTTTTGCCCTGGTCTATTCA
Found at i:751223 original size:15 final size:15
Alignment explanation
Indices: 751203--751243 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
751193 TGGGACTGGG
*
751203 GCCCTTGGAATAGGT
1 GCCCTTGGAACAGGT
751218 GCCCTTGGAACAGGT
1 GCCCTTGGAACAGGT
*
751233 GCCCTAGGAAC
1 GCCCTTGGAAC
751244 TGTGCCCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.20
Consensus pattern (15 bp):
GCCCTTGGAACAGGT
Found at i:751784 original size:102 final size:102
Alignment explanation
Indices: 751597--751800 Score: 300
Period size: 102 Copynumber: 2.0 Consensus size: 102
751587 ACAGAGGTAT
* *
751597 TTGTCAACTGTGGAGCCTGTGATTGTGGATATGGCTGCTGAACAGAAGTCATTGTCATCTGTGGA
1 TTGTCAACTGTGGAGCATGTGATTGCGGATATGGCTGCTGAACAGAAGTCATTGTCATCTGTGGA
** * * *
751662 GCCTGTGATTGCGGATATGGTTGCTGGACAGAGGCCA
66 GCCTGTGAGAGCGGAAATGGTTGCTGCACAGAAGCCA
* *
751699 TTGTCATCTGTGGAGCATGTGATTGCGGATATGGTTGCTGAACAGAAGTCATTGTCATCTGTGGA
1 TTGTCAACTGTGGAGCATGTGATTGCGGATATGGCTGCTGAACAGAAGTCATTGTCATCTGTGGA
* * *
751764 GCTTGTGAGAGGGGAAATGGTTGTTGCACAGAAGCCA
66 GCCTGTGAGAGCGGAAATGGTTGCTGCACAGAAGCCA
751801 GAGTTGGAAC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.29
Consensus pattern (102 bp):
TTGTCAACTGTGGAGCATGTGATTGCGGATATGGCTGCTGAACAGAAGTCATTGTCATCTGTGGA
GCCTGTGAGAGCGGAAATGGTTGCTGCACAGAAGCCA
Found at i:751797 original size:51 final size:51
Alignment explanation
Indices: 751597--751771 Score: 278
Period size: 51 Copynumber: 3.4 Consensus size: 51
751587 ACAGAGGTAT
* * *
751597 TTGTCAACTGTGGAGCCTGTGATTGTGGATATGGCTGCTGAACAGAAGTCA
1 TTGTCATCTGTGGAGCCTGTGATTGCGGATATGGTTGCTGAACAGAAGTCA
* * *
751648 TTGTCATCTGTGGAGCCTGTGATTGCGGATATGGTTGCTGGACAGAGGCCA
1 TTGTCATCTGTGGAGCCTGTGATTGCGGATATGGTTGCTGAACAGAAGTCA
*
751699 TTGTCATCTGTGGAGCATGTGATTGCGGATATGGTTGCTGAACAGAAGTCA
1 TTGTCATCTGTGGAGCCTGTGATTGCGGATATGGTTGCTGAACAGAAGTCA
*
751750 TTGTCATCTGTGGAGCTTGTGA
1 TTGTCATCTGTGGAGCCTGTGA
751772 GAGGGGAAAT
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 113 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (51 bp):
TTGTCATCTGTGGAGCCTGTGATTGCGGATATGGTTGCTGAACAGAAGTCA
Found at i:764640 original size:84 final size:84
Alignment explanation
Indices: 764499--764720 Score: 259
Period size: 84 Copynumber: 2.6 Consensus size: 84
764489 CTTTGTCCAT
* * * **
764499 ATTTTCGACAGTGAATAACTCTTCAGTGACTTTGAACTTG-TTGGGATCTTCTTTTGTTGGTTTT
1 ATTTTCCACAGAGAACAACTCTTCAGTGACTTTGAACTTGTTTGGG-TCTTCTTTTGTTACTTTT
* * **
764563 CTCT-TACCAGTATCTTTTAC
65 CT-TGTACCAGCACCTTCAAC
*
764583 ATTTTCCACAGAGAACATCTCTTCAGTGACTTTGAACTTGTTTGGGTCTTCTTTTGTTACTTTTC
1 ATTTTCCACAGAGAACAACTCTTCAGTGACTTTGAACTTGTTTGGGTCTTCTTTTGTTACTTTTC
*
764648 TTGTTCCAGCACCTTCAAC
66 TTGTACCAGCACCTTCAAC
* * * * * *
764667 ATTTTCCACAGTGAATAACTCTTCAGTAACTTTAAATTTGTTGGGGTCTTCTTT
1 ATTTTCCACAGAGAACAACTCTTCAGTGACTTTGAACTTGTTTGGGTCTTCTTT
764721 GGCGGGTCTT
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
83 1 0.01
84 112 0.95
85 5 0.04
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (84 bp):
ATTTTCCACAGAGAACAACTCTTCAGTGACTTTGAACTTGTTTGGGTCTTCTTTTGTTACTTTTC
TTGTACCAGCACCTTCAAC
Found at i:765529 original size:30 final size:30
Alignment explanation
Indices: 765493--765584 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 30
765483 ATATCGACTG
*
765493 TCCTTTGATCTACTTCTGTCTTGTCT-CTTA
1 TCCTTTGATCTACTCCTGTCTTGTCTAC-TA
765523 TCCTTTGATCTACTCCTGTCTTGTCTACTA
1 TCCTTTGATCTACTCCTGTCTTGTCTACTA
* *
765553 TCCTTTGATCTACTCCTGTCTCGTCTTCTA
1 TCCTTTGATCTACTCCTGTCTTGTCTACTA
765583 TC
1 TC
765585 ACTTCTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 57 0.98
31 1 0.02
ACGTcount: A:0.11, C:0.30, G:0.10, T:0.49
Consensus pattern (30 bp):
TCCTTTGATCTACTCCTGTCTTGTCTACTA
Found at i:767052 original size:21 final size:21
Alignment explanation
Indices: 766958--767052 Score: 56
Period size: 21 Copynumber: 4.6 Consensus size: 21
766948 GTCAACTGGT
**
766958 AACTATAGTTT-ACGAAACGTA
1 AACTATAGTTTAACG-ATTGTA
* *
766979 AACTATAG-TTAACGATTCTTT
1 AACTATAGTTTAACGATT-GTA
* *
767000 AACTAAAGTTT-TC-ATCTGTAA
1 AACTATAGTTTAACGAT-TGT-A
*
767021 AACCATA-TTTAACGATTGTA
1 AACTATAGTTTAACGATTGTA
767041 AACTATAGTTTA
1 AACTATAGTTTA
767053 CGAATGCTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
20 16 0.30
21 34 0.63
22 4 0.07
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (21 bp):
AACTATAGTTTAACGATTGTA
Found at i:768751 original size:158 final size:162
Alignment explanation
Indices: 768439--768768 Score: 470
Period size: 158 Copynumber: 2.0 Consensus size: 162
768429 ATGAAGGCCA
* *
768439 AAATATGGAATACAGGATGTTCGCCAGCCCCTTTAAAGATATCCCATTATAACTGTATTATAAAA
1 AAATATGGAATACAGGATGTTAGCCAGCCCCTTTAAAGATATCCCATTATAACTGTATTACAAAA
* * * *
768504 AATGTCCTATTTTTGCCAGGCTAGCTAAGCCTCTTACTGGTCGTGTAAACCCATTTTCTTTTGAG
66 AATGTCCCATTTTT-CCA-GCCA-CTAAGCCTCTTACTGGTCGTGTAAACCCAATTTCTTTTCAG
*
768569 GATTGACTGGGCGTTACCGGGGCCCCATCCCCACC
128 GATCGACTGGGCGTTACCGGGGCCCCATCCCCACC
* * * *
768604 AAATATGGAATGCAGGGTGTTAGCCAGCTCCTTTAAAGATATCCCATTATAACTGTATTACACAA
1 AAATATGGAATACAGGATGTTAGCCAGCCCCTTTAAAGATATCCCATTATAACTGTATTACAAAA
* *
768669 AATGTCCCA-TTTT-C-GCCA-TAAGCCTTTTACTGGTCGTGTAAACCCAATTTCTTTTCAGGGT
66 AATGTCCCATTTTTCCAGCCACTAAGCCTCTTACTGGTCGTGTAAACCCAATTTCTTTTCAGGAT
* *
768730 CGACTGGGCGTTGCCGTGGCCCCATCCCCACC
131 CGACTGGGCGTTACCGGGGCCCCATCCCCACC
768762 AAATATG
1 AAATATG
768769 AAGGCCCAAA
Statistics
Matches: 150, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
158 75 0.50
160 3 0.02
162 1 0.01
164 4 0.03
165 67 0.45
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (162 bp):
AAATATGGAATACAGGATGTTAGCCAGCCCCTTTAAAGATATCCCATTATAACTGTATTACAAAA
AATGTCCCATTTTTCCAGCCACTAAGCCTCTTACTGGTCGTGTAAACCCAATTTCTTTTCAGGAT
CGACTGGGCGTTACCGGGGCCCCATCCCCACC
Found at i:778729 original size:75 final size:75
Alignment explanation
Indices: 778606--778761 Score: 294
Period size: 75 Copynumber: 2.1 Consensus size: 75
778596 ATGAAATGCT
778606 ATAGCTACTGAATTCTCTTGTATCACTTGACAGTAGGCTCCTTTAACTTATCTACAGAGGATTAT
1 ATAGCTACTGAATTCTCTTGTATCACTTGACAGTAGGCTCCTTTAACTTATCTACAGAGGATTAT
778671 CAGTATTGCA
66 CAGTATTGCA
*
778681 ATAGCTACTGAATTCTCTTGTATCACTTGACAGTGGGCTCCTTTAACTTATCTACAGAGGATTAT
1 ATAGCTACTGAATTCTCTTGTATCACTTGACAGTAGGCTCCTTTAACTTATCTACAGAGGATTAT
778746 CAGTATTGCA
66 CAGTATTGCA
*
778756 AGAGCT
1 ATAGCT
778762 TACACAATGG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (75 bp):
ATAGCTACTGAATTCTCTTGTATCACTTGACAGTAGGCTCCTTTAACTTATCTACAGAGGATTAT
CAGTATTGCA
Found at i:789271 original size:2 final size:2
Alignment explanation
Indices: 789266--789336 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
789256 AATCAAAATA
789266 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
789308 AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
789337 ATATGAAACT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:796941 original size:2 final size:2
Alignment explanation
Indices: 796934--796986 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
796924 TTACTTCAAT
796934 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
796976 GA GA GA GA GA G
1 GA GA GA GA GA G
796987 TGTGCAACAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:797606 original size:2 final size:2
Alignment explanation
Indices: 797599--797646 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
797589 ACTGGTCTCC
* * *
797599 AG AG AG AG AG AG AG AA AG AG AA AG AG AT AG AG AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
797640 AG AG AG A
1 AG AG AG A
797647 AAATACAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (2 bp):
AG
Found at i:800127 original size:8 final size:8
Alignment explanation
Indices: 800114--800152 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
800104 TTTCCTCTGC
800114 GTCCGTCA
1 GTCCGTCA
*
800122 GTCCGTCT
1 GTCCGTCA
* *
800130 GTCTGTCC
1 GTCCGTCA
800138 GTCCGTCA
1 GTCCGTCA
800146 GTCCGTC
1 GTCCGTC
800153 TGTCTGTCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.05, C:0.38, G:0.26, T:0.31
Consensus pattern (8 bp):
GTCCGTCA
Found at i:800137 original size:12 final size:12
Alignment explanation
Indices: 800122--800161 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
800112 GCGTCCGTCA
800122 GTCCGTCTGTCT
1 GTCCGTCTGTCT
* *
800134 GTCCGTCCGTCA
1 GTCCGTCTGTCT
800146 GTCCGTCTGTCT
1 GTCCGTCTGTCT
800158 GTCC
1 GTCC
800162 CACTTCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.38, G:0.25, T:0.35
Consensus pattern (12 bp):
GTCCGTCTGTCT
Found at i:800140 original size:24 final size:24
Alignment explanation
Indices: 800113--800161 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
800103 CTTTCCTCTG
800113 CGTCCGTCAGTCCGTCTGTCTGTC
1 CGTCCGTCAGTCCGTCTGTCTGTC
800137 CGTCCGTCAGTCCGTCTGTCTGTC
1 CGTCCGTCAGTCCGTCTGTCTGTC
800161 C
1 C
800162 CACTTCAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.04, C:0.39, G:0.24, T:0.33
Consensus pattern (24 bp):
CGTCCGTCAGTCCGTCTGTCTGTC
Found at i:800952 original size:2 final size:2
Alignment explanation
Indices: 800945--801004 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
800935 GGACTATTAC
800945 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
800987 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
801005 TCAGATTTGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:804685 original size:2 final size:2
Alignment explanation
Indices: 804678--804720 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
804668 TATTCTCAGC
804678 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
804720 C
1 C
804721 ATATGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:812724 original size:14 final size:15
Alignment explanation
Indices: 812700--812728 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
812690 TCTTTCAAAT
812700 AAAATTGAAAAAAAA
1 AAAATTGAAAAAAAA
812715 AAAATT-AAAAAAAA
1 AAAATTGAAAAAAAA
812729 TTCTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAATTGAAAAAAAA
Found at i:814240 original size:27 final size:28
Alignment explanation
Indices: 814190--814245 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
814180 TTTCTGATAA
814190 TACTAATGCTTAAAAAAAAAAGCATCAT
1 TACTAATGCTTAAAAAAAAAAGCATCAT
814218 TACTAATGCTT-AAAAAAAAAGCATCAT
1 TACTAATGCTTAAAAAAAAAAGCATCAT
814245 T
1 T
814246 TATATGTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (28 bp):
TACTAATGCTTAAAAAAAAAAGCATCAT
Found at i:819982 original size:29 final size:29
Alignment explanation
Indices: 819950--820153 Score: 99
Period size: 29 Copynumber: 7.1 Consensus size: 29
819940 GTAACAGTAC
* *
819950 TGCTATGGAGATGTATAGGGCCAAAATGT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
* * * * * * *
819979 TGCTTTGG-GATGTCTAAGATGACAGTAT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
** * *
820007 CACTAAGGAGATGTATAGGGCCAAAATAT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
* * * * **
820036 TGCTTTGG-GATGTCTAAGGTGATCATAT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
* * * *
820064 TGCTAAGGAGATGAATAGGGCCAAAATGT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
* * * * ***
820093 TGCTTTGG-GATGTCTAAGGTGACCGTAT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
* *
820121 TGCTAAGGAGATGTATAGGGTCAAAATGT
1 TGCTATGGAGATGTATAGGGTCAAAATAT
820150 TGCT
1 TGCT
820154 TTGGGTTGTC
Statistics
Matches: 112, Mismatches: 60, Indels: 6
0.63 0.34 0.03
Matches are distributed among these distances:
28 53 0.47
29 59 0.53
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.30
Consensus pattern (29 bp):
TGCTATGGAGATGTATAGGGTCAAAATAT
Found at i:820004 original size:57 final size:57
Alignment explanation
Indices: 819943--820424 Score: 538
Period size: 57 Copynumber: 8.3 Consensus size: 57
819933 TTCCAAAGTA
* *
819943 ACAGTACTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGATG
1 ACAGTATTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGGTG
** * *
820000 ACAGTATCACTAAGGAGATGTATAGGGCCAAAATATTGCTTTGGGATGTCTAAGGTG
1 ACAGTATTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGGTG
* *
820057 ATCA-TATTGCTAAGGAGATGAATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGGTG
1 A-CAGTATTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGGTG
* * * * *
820114 ACCGTATTGCTAAGGAGATGTATAGGGTCAAAATGTTGCTTTGGGTTGTCAAAGGTG
1 ACAGTATTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGGTG
* * * * *
820171 ACCGTATTGCTAAGGAGATGTATAGGGCCAAAGTGTTGCTTTGAGGATGCCAAAGGTG
1 ACAGTATTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTG-GGATGTCTAAGGTG
* * * *
820229 CCAGTATTGCTATGG-GAAAGTATAGGGCAAAAATGTTGCTTTTGGGATGTCAAAGGTG
1 ACAGTATTGCTATGGAG-ATGTATAGGGCCAAAATGTTGC-TTTGGGATGTCTAAGGTG
* * * * * * *
820287 CCAGTATTGCTATGGGGAATTTATAGGGCCAGTTATTGTTGCTTTGGTAAGGTCTAAGGTG
1 ACAGTATTGCTATGGAG-ATGTATAGGGCCA--AAATGTTGCTTTGG-GATGTCTAAGGTG
* * * *
820348 CCTGTATTGCTATGG-GAAAGTATAGGGCAAAAATGTTGCTTTGGGGATGTCTAAGGTG
1 ACAGTATTGCTATGGAG-ATGTATAGGGCCAAAATGTTGCTTT-GGGATGTCTAAGGTG
* *
820406 CCAGTATTGTTATGGAGAT
1 ACAGTATTGCTATGGAGAT
820425 ATCTTATGTG
Statistics
Matches: 369, Mismatches: 45, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
56 1 0.00
57 193 0.52
58 108 0.29
59 19 0.05
60 17 0.05
61 31 0.08
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.30
Consensus pattern (57 bp):
ACAGTATTGCTATGGAGATGTATAGGGCCAAAATGTTGCTTTGGGATGTCTAAGGTG
Found at i:820048 original size:28 final size:28
Alignment explanation
Indices: 820016--820105 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
820006 TCACTAAGGA
820016 GATGTATAGGGCCAAAATATTGCTTTGG
1 GATGTATAGGGCCAAAATATTGCTTTGG
* * ** ** **
820044 GATGTCTAAGGTGATCATATTGCTAAGG
1 GATGTATAGGGCCAAAATATTGCTTTGG
* *
820072 AGATGAATAGGGCCAAAATGTTGCTTTGG
1 -GATGTATAGGGCCAAAATATTGCTTTGG
820101 GATGT
1 GATGT
820106 CTAAGGTGAC
Statistics
Matches: 42, Mismatches: 19, Indels: 2
0.67 0.30 0.03
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.31
Consensus pattern (28 bp):
GATGTATAGGGCCAAAATATTGCTTTGG
Found at i:820123 original size:28 final size:28
Alignment explanation
Indices: 820092--820181 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
820082 GGCCAAAATG
820092 TTGCTTTGGGATGTCTAAGGTGACCGTA
1 TTGCTTTGGGATGTCTAAGGTGACCGTA
** * * * *** *
820120 TTGCTAAGGAGATGTATAGGGTCAAAATG
1 TTGCTTTGG-GATGTCTAAGGTGACCGTA
* *
820149 TTGCTTTGGGTTGTCAAAGGTGACCGTA
1 TTGCTTTGGGATGTCTAAGGTGACCGTA
820177 TTGCT
1 TTGCT
820182 AAGGAGATGT
Statistics
Matches: 41, Mismatches: 20, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
28 22 0.54
29 19 0.46
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (28 bp):
TTGCTTTGGGATGTCTAAGGTGACCGTA
Found at i:820304 original size:29 final size:29
Alignment explanation
Indices: 820160--820304 Score: 75
Period size: 29 Copynumber: 5.0 Consensus size: 29
820150 TGCTTTGGGT
* *
820160 TGTCAAAGGTGACC-GTATTGCTAAGGAGA
1 TGTCAAAGGTG-CCAGTATTGCTATGGGGA
* * * *
820189 TGT-ATAGG-GCCAAAGTGTTGCTTTGAGGA
1 TGTCAAAGGTGCC--AGTATTGCTATGGGGA
* *
820218 TGCCAAAGGTGCCAGTATTGCTATGGGAA
1 TGTCAAAGGTGCCAGTATTGCTATGGGGA
* * * * * * *
820247 AGT-ATAGG-GCAAAAATGTTGCTTTTGGGA
1 TGTCAAAGGTGC--CAGTATTGCTATGGGGA
820276 TGTCAAAGGTGCCAGTATTGCTATGGGGA
1 TGTCAAAGGTGCCAGTATTGCTATGGGGA
820305 ATTTATAGGG
Statistics
Matches: 79, Mismatches: 28, Indels: 18
0.63 0.22 0.14
Matches are distributed among these distances:
26 2 0.03
27 3 0.04
28 8 0.10
29 53 0.67
30 8 0.10
31 5 0.06
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (29 bp):
TGTCAAAGGTGCCAGTATTGCTATGGGGA
Found at i:820692 original size:24 final size:26
Alignment explanation
Indices: 820660--820728 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 26
820650 CTAAAATCAA
*
820660 TATTACTATGGAGATGG-C-TTACAG
1 TATTGCTATGGAGATGGCCGTTACAG
820684 TATTGCTATGGAGATGGCCTGGGTTACAG
1 TATTGCTATGGAGATGGCC---GTTACAG
*
820713 TATTGCTATAGAGATG
1 TATTGCTATGGAGATG
820729 CCTTTGGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 16 0.42
25 1 0.03
29 21 0.55
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (26 bp):
TATTGCTATGGAGATGGCCGTTACAG
Found at i:821857 original size:167 final size:163
Alignment explanation
Indices: 821370--822116 Score: 656
Period size: 167 Copynumber: 4.5 Consensus size: 163
821360 TGCGTCCAAA
* * ** * * *
821370 TGGTACAAAAATAGATCCTAACGTATGGCATGCCTTACCAAATAGTGTGTTAAAATTTCAAGCAT
1 TGGT-CAAAAATATATCCAAATATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCCAGCAT
* * * * *
821435 CTGCAATGAATACATGTAATTGCTGAGAAATCTTTAACAAAAATTTGTTTAAAAATTTAGGCTAA
65 CTGCGATGAAT--A-G---TTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTAGGC-AA
* ** * * * * * ** **
821500 AAGTAAACGATGTCATCACTTAACAGGAAGTTTATGTCCAAT
123 AAATAAATAAAGTC-TTATTTAATAGGAAGTTGACATCTGAT
* * * * ** * *
821542 T-AT-GAAAATAGATCCTAACGTATGGCATGCCTAAACAAATAATATGTTAAAATTTCCAGCATC
1 TGGTCAAAAATATATCCAAATATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCCAGCATC
*
821605 TAGCTGCAATGAATAGTTGCTGAGAAATCTTTGACG-AAATTTGTTTGAAAATTT-GGACTAAAA
66 T-GC-G--ATGAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTAGG-C-AAAA
*
821668 ATAAACAAAGTCGTTATTTAATAGGAAGTTGACATCTGAT
125 ATAAATAAAGTC-TTATTTAATAGGAAGTTGACATCTGAT
* * *
821708 TGGTCTAAAAATATATCCGAAATATATGGCATGCTTAAATAAATAGTGTG-TAAACATTTCCAGT
1 TGGTC-AAAAATATATCC-AAATATATGGCATGCCTAAACAAATAGTGTGTTAAA-ATTTCCAGC
*
821772 ATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTAGGCAATAAAT
63 ATCTGCGATGAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTAGGCAA-AAAT
* *
821837 AAATAAAGTCATTATTTAATAGGAAGTTGACATCCGAG
127 AAATAAAGTC-TTATTTAATAGGAAGTTGACATCTGAT
* * * * *
821875 TGGTCCAAAAATATATCCAAAATATATGGCATGCCTTAACAAATAGCGTGTTAACATCTCTAGCA
1 TGGT-CAAAAATATATCC-AAATATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCCAGCA
* * *
821940 TCTGC----AATAGTTGCCAAGAAATCTTTGACGAAAATTTGCTTGAAAATTTAGGC---AAGAA
64 TCTGCGATGAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTAGGCAAAAATAA
* * *
821998 ATAAAGTCTTCATTTAACAGGAAGTTGACGT-TAAAT
129 ATAAAGTCTT-ATTTAATAGGAAGTTGACATCT-GAT
* * * * *
822034 TGGTACAAAAATACATCCCAACATATGGCATGCCTAAGCAAAGAGTGTGTTAAAATTTCCAGCAT
1 TGGT-CAAAAATATATCCAAATATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCCAGCAT
*
822099 CTGCGATGAATTGTTGCT
65 CTGCGATGAATAGTTGCT
822117 GAAAAAAATG
Statistics
Matches: 484, Mismatches: 70, Indels: 52
0.80 0.12 0.09
Matches are distributed among these distances:
158 44 0.09
159 47 0.10
162 8 0.02
163 46 0.10
165 2 0.00
166 80 0.17
167 131 0.27
168 7 0.01
169 71 0.15
170 39 0.08
171 2 0.00
172 1 0.00
173 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (163 bp):
TGGTCAAAAATATATCCAAATATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCCAGCATC
TGCGATGAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTAGGCAAAAATAAAT
AAAGTCTTATTTAATAGGAAGTTGACATCTGAT
Found at i:823817 original size:31 final size:31
Alignment explanation
Indices: 823779--823867 Score: 169
Period size: 31 Copynumber: 2.9 Consensus size: 31
823769 CCATATTAAC
*
823779 CAATTTAGTTTGTCATACTGTATGGTTAGTA
1 CAATTTAGTTTGCCATACTGTATGGTTAGTA
823810 CAATTTAGTTTGCCATACTGTATGGTTAGTA
1 CAATTTAGTTTGCCATACTGTATGGTTAGTA
823841 CAATTTAGTTTGCCATACTGTATGGTT
1 CAATTTAGTTTGCCATACTGTATGGTT
823868 TGAAAGAACA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (31 bp):
CAATTTAGTTTGCCATACTGTATGGTTAGTA
Found at i:833800 original size:180 final size:179
Alignment explanation
Indices: 833496--834041 Score: 939
Period size: 180 Copynumber: 3.0 Consensus size: 179
833486 GTGAAATGGA
* *
833496 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
1 GTACCCTGTATGCAATATTTTGCCAAAAAATGACTAAGTTCGAAAGCTGGTATTTTTTCATAAAT
* *
833561 AATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTAATCTGCAAAAGA
66 TATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTAATCTGCAAAAGA
833626 ACAACTTCCTATCTTCAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
131 ACAACTTCCTATCTTCAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
* *
833675 GTACCCTGTATGCAATATTTTGCCAAATAATGACCAAGTTCGAAAGCTGGTATATTTTTCATAAA
1 GTACCCTGTATGCAATATTTTGCCAAAAAATGACTAAGTTCGAAAGCTGGTAT-TTTTTCATAAA
* * ** * *
833740 TTATCGGAAATCAAAATTCTAGCAATATGTACACCTCTTTTATAAGTACAATTGATCTGCAAAAG
65 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTAATCTGCAAAAG
*
833805 AACAACTTCCTATTTTCAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
130 AACAACTTCCTATCTTCAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
*
833855 GTACCCTGTATGCAATATTTTGCCAAAAAATGACTAAGTTCGAAAGCTGGTATTTTGGTCATAAA
1 GTACCCTGTATGCAATATTTTGCCAAAAAATGACTAAGTTCGAAAGCTGGTATTTT-TTCATAAA
833920 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTAATCTGCAAAAG
65 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTAATCTGCAAAAG
*
833985 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
130 AACAACTTCCTATCTTCAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
834035 GTACCCT
1 GTACCCT
834042 TTTGGCAGCC
Statistics
Matches: 341, Mismatches: 24, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
179 52 0.15
180 289 0.85
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (179 bp):
GTACCCTGTATGCAATATTTTGCCAAAAAATGACTAAGTTCGAAAGCTGGTATTTTTTCATAAAT
TATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTAATCTGCAAAAGA
ACAACTTCCTATCTTCAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
Found at i:843469 original size:4 final size:4
Alignment explanation
Indices: 843453--843537 Score: 102
Period size: 4 Copynumber: 21.8 Consensus size: 4
843443 AACTAAATAT
* *
843453 GAGA GAGA CAGA GAGA GAGA CAGA GAGA -AG- GAGA GAGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * *
843499 GAGA GAGA GAGA GAGA GAGA CAGA CAGA CAGA CAGA GAG
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAG
843538 TGCAACAATA
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
3 4 0.05
4 69 0.95
ACGTcount: A:0.49, C:0.07, G:0.44, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:846935 original size:11 final size:11
Alignment explanation
Indices: 846919--846943 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
846909 CTTTTTGTGT
846919 ATAAAAAAAAA
1 ATAAAAAAAAA
846930 ATAAAAAAAAA
1 ATAAAAAAAAA
846941 ATA
1 ATA
846944 TGGTCAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (11 bp):
ATAAAAAAAAA
Found at i:850949 original size:12 final size:12
Alignment explanation
Indices: 850922--850962 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
850912 ATATATCTCG
850922 AATAA-ACAT-T
1 AATAACACATAT
850932 ATATAACACATAT
1 A-ATAACACATAT
*
850945 AATAATACATAT
1 AATAACACATAT
850957 AATAAC
1 AATAAC
850963 TAGAGGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 4 0.15
12 19 0.73
13 2 0.08
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAACACATAT
Found at i:851632 original size:146 final size:146
Alignment explanation
Indices: 851300--852009 Score: 930
Period size: 146 Copynumber: 4.9 Consensus size: 146
851290 TTTTTAACAA
* * * * * * *
851300 TGACCTTGAACTT-CCTCAATTGACCTTTGGTCAAGGTCATGACACACTCTCAGGTTATAAGCAT
1 TGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* * ** * * ** *
851364 TC-TAGATGTGAATTAAGAACTTCCAATACTTGTCCATTAGAAAGATATGGACTGGACACGAGTT
65 TCTTTG-TGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATT
* *
851428 TTACAC-TTTTCTGCAAG
129 TTGCACTTTTTCTGCCAG
* * *
851445 TGACCTTGGCCTTGCCCAAATGACCTTGGGTGAAGGTCATGAC-CAACCCTTAGCTCATAAGCAA
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACAC-ACCCTTAGGTCATAAGCAA
* * * * *
851509 TCTTTGTGTGAACTGAGAACTTCCAACGTTTCTCCATAAGAAAGATATGGACCAGACAAGAACTT
65 TCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTT
* * *
851574 TGCATTTTTTCGGCCAT
130 TGCACTTTTTCTGCCAG
*
851591 TGACCTTGACCTTGTCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
851656 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATTAA-AAAGATATGGACCAGACACGAATTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCA-TAAGAAAGATATGGACCAGACACGAATTT
* *
851720 TACACTTTTTCTGTCAG
130 TGCACTTTTTCTGCCAG
* * * *
851737 TGACCTTGCCCTTGCCCGAATGACCTTGGGTTAAGGTCATGACACACCCTTAAGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
*
851802 CTTTGTGTGAAGTAA-AATCTTCCAATGTTTCTCCATAAGATAA-ATATGGACCGGACACGAATT
66 CTTTGTGTGAAGTAAGAA-CTTCCAATGTTTCTCCATAAGA-AAGATATGGACCAGACACGAATT
851865 TTGCACTTTTTCTGCCAG
129 TTGCACTTTTTCTGCCAG
* * *
851883 TGACCTTGACCTTGCCCGAATGACCTTGGTTCAAGGTCTTGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * *
851948 CTTTGTGTGAAGTAAGAACCTCTAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAAT
852010 CGAACAGACA
Statistics
Matches: 497, Mismatches: 57, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
144 1 0.00
145 108 0.22
146 380 0.76
147 8 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTTT
GCACTTTTTCTGCCAG
Found at i:852030 original size:12 final size:12
Alignment explanation
Indices: 852013--852067 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
852003 CACGAATCGA
852013 ACAGACAGACGG
1 ACAGACAGACGG
*
852025 ACAGACGGACGG
1 ACAGACAGACGG
*
852037 ACGGAC-GTACGG
1 ACAGACAG-ACGG
*
852049 ACAGACGGACGG
1 ACAGACAGACGG
*
852061 ACGGACA
1 ACAGACA
852068 AGGTGATTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 1 0.03
12 34 0.94
13 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.38, T:0.02
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:852035 original size:4 final size:4
Alignment explanation
Indices: 852020--852066 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
852010 CGAACAGACA
* * *
852020 GACG GACA GACG GACG GACG GACG TACG GACA GACG GACG GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
852067 AAGGTGATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.43, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:856697 original size:18 final size:18
Alignment explanation
Indices: 856670--856710 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
856660 CTCCAGATTT
*
856670 AGCTATATAGCTTGAATA
1 AGCTAAATAGCTTGAATA
* *
856688 AGCTAAATAGCTTTATTA
1 AGCTAAATAGCTTGAATA
856706 AGCTA
1 AGCTA
856711 TTCAGAGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (18 bp):
AGCTAAATAGCTTGAATA
Found at i:857271 original size:18 final size:18
Alignment explanation
Indices: 857248--857289 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
857238 GCTATTTTGA
*
857248 ATAGCTTTATAAAGCTCT
1 ATAGCTTTATAAAGCTAT
* *
857266 ATAGCTTTTTGAAGCTAT
1 ATAGCTTTATAAAGCTAT
857284 ATAGCT
1 ATAGCT
857290 AAATCAAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (18 bp):
ATAGCTTTATAAAGCTAT
Found at i:857651 original size:67 final size:67
Alignment explanation
Indices: 857572--857706 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
857562 ATATGTCAGT
*
857572 CAGAATCTGGTATGTGTTGTTTTATATATTGCATGCAGTTTTGTTTTTATTTATTTGATGTTGTA
1 CAGAATCTGGTATGTGTTGTTTTATATATTGCATGCAGTTTTATTTTTATTTATTTGATGTTGTA
857637 GG
66 GG
857639 CAGAATCTGGTATGTGTTGTTTTATATATTGCATGCAGTTTTATTTTTATTTATTTGATGTTGTA
1 CAGAATCTGGTATGTGTTGTTTTATATATTGCATGCAGTTTTATTTTTATTTATTTGATGTTGTA
857704 GG
66 GG
857706 C
1 C
857707 CTATTTAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.20, C:0.07, G:0.21, T:0.52
Consensus pattern (67 bp):
CAGAATCTGGTATGTGTTGTTTTATATATTGCATGCAGTTTTATTTTTATTTATTTGATGTTGTA
GG
Found at i:877584 original size:146 final size:146
Alignment explanation
Indices: 877320--878021 Score: 1051
Period size: 146 Copynumber: 4.9 Consensus size: 146
877310 GTCTGTGCAA
* *
877320 TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGAAAGTTCTTACTTCACACAAAGATGGC
1 TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
**
877385 TTATGACCTAAGGGTGTGTCATGACCTTGACTTAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
877450 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* *
877466 TCGTGTCTGGTCCATATCTTTCTTGTGGAAAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * * *
877531 TTATGGCCTAAGGGTGTGTCTTGATCTTTACCCAAGGTCATTTGAGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
877596 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* * * *
877612 TTGTGTCGGGTCCATATCTTTCTTATGGAGAAACATTGGAATTTCTTACTACACACAAAGATTGC
1 TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
** * *
877677 TTATGACCTAAGGGTGTGTCATGACCTTGACTTAAGGTCATTCGGGCAAGGTTAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
877742 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* * *
877758 TCGTGTCTGGTCCATATCTTTCTTGTGGAAAAACATTGGAAGTTCTTACTTCACACAAAGATTAC
1 TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * *
877823 TTATGGCCTAAGGGTGTGTCTTGACCTTGACCCAAGGTCATTTGGGCAAGGTCAATGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
877888 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* *
877904 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAAC------A-TTCTTACTTCACACAAAGTTTGC
1 TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * * *
877962 TTATGACCAAAGGGTGTGTCATGACCTTTACCCAAGGTAAATTGAGG-AAGTTCAAGGTCA
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTG-GGCAAGGTCAAGGTCA
878022 TTGTTTCAAA
Statistics
Matches: 502, Mismatches: 53, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
139 70 0.14
140 3 0.01
146 429 0.85
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (146 bp):
TCGTGTCTGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATGCAAAAT
Found at i:884035 original size:16 final size:16
Alignment explanation
Indices: 884014--884047 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
884004 CGGACCGGTG
884014 GATGGAAGGAAGGACA
1 GATGGAAGGAAGGACA
*
884030 GATGGATGGAAGGACA
1 GATGGAAGGAAGGACA
884046 GA
1 GA
884048 CTGATCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.44, T:0.09
Consensus pattern (16 bp):
GATGGAAGGAAGGACA
Found at i:884594 original size:16 final size:15
Alignment explanation
Indices: 884567--884601 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
884557 GATCACTTTT
884567 TGTCCGGCGTCCGTC
1 TGTCCGGCGTCCGTC
884582 TGTCCGTGCGTCCGTC
1 TGTCCG-GCGTCCGTC
884598 TGTC
1 TGTC
884602 TTCTCCTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.00, C:0.37, G:0.31, T:0.31
Consensus pattern (15 bp):
TGTCCGGCGTCCGTC
Found at i:885548 original size:166 final size:166
Alignment explanation
Indices: 884955--885611 Score: 1021
Period size: 166 Copynumber: 4.0 Consensus size: 166
884945 GGAGTATATA
* *
884955 TAAAAATCTTCTTCTCAAAAATCATTTGACCAGAAAAGCTGAAACTTGTGTTGAAGCATCCTCAG
1 TAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * * * *
885020 ATAGTGTAGGTACAAGTTTGTTCAAATCATAGTCCTTGGGGGTAAGGTGGGGCCTCAATAGGGGG
66 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAAT--GGGG
885085 GGTCAAAGTTTTACATAGGAGTATATAGAGTTAATCTT
129 GGTCAAAGTTTTACATAGGAGTATATAGAGTTAATCTT
* * *
885123 TAAAAATCTTCTTCTCAAAAACCATTCGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAG
1 TAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* **
885188 ATAGTGTAGGTTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGGGTT
66 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGGGGG
** *
885253 TTGAATTTTTACATAGGAGTATATAGAGTTAATCTT
131 TCAAAGTTTTACATAGGAGTATATAGAGTTAATCTT
* * *
885289 CTAAAAA--ATCTTCTCAAAAGCCATTTGACCAGAAAAGCCGAAACTTGTGTGGAAGCATCCTCA
1 -TAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCA
*
885352 GATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGG
65 GATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGGGG
**
885417 GTCAAAGTTTTACATATAAGTATATAGAGTTAATCTT
130 GTCAAAGTTTTACATAGGAGTATATAGAGTTAATCTT
885454 TAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 TAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * *
885519 ATGGTGTAGATTTATGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGGGGG
66 ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGGGGG
* * *
885584 TCAAATTTTTACATAGGAATATAAAGAG
131 TCAAAGTTTTACATAGGAGTATATAGAG
885612 AAATTTTATT
Statistics
Matches: 445, Mismatches: 41, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
164 6 0.01
165 143 0.32
166 175 0.39
167 6 0.01
168 115 0.26
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (166 bp):
TAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
ATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGGGGG
TCAAAGTTTTACATAGGAGTATATAGAGTTAATCTT
Found at i:885631 original size:331 final size:330
Alignment explanation
Indices: 884862--885633 Score: 1139
Period size: 331 Copynumber: 2.4 Consensus size: 330
884852 CAGAGAGCTA
* *
884862 CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCCGGGGGTAAGGTGGGGCCACAATGGG
1 CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGG
* * * *
884927 GGGTCAAAGTTTTACATAGGAGTATATATA-AAA---A-TCT---TCTTCTCAAAAATCATTTGA
66 GGGTCAAATTTTTACATAGGAGTATATAGAGAAATTTATTATAAATCTTCTCAAAAACCATTTGA
* * *
884984 CCAGAAAAGCTGAAACTTGTGTTGAAGCATCCTCAGATAGTGTAGGTACAAGTTTGTTCAAATCA
131 CCAGAAAAGCCGAAACTTGTGTGGAAGCATCCTCAGATAGTGTAGATACAAGTTTGTTCAAATCA
* *
885049 TAGTCCTTGGGGGTAAGGTGGGGCCTCAATAGGGGGGGTCAAAGTTTTACATAGGAGTATATAGA
196 TAGTCCCTGGGGGTAAGGTGGGGCCTCAATA-GGGGGGTCAAAGTTTTACATAGAAGTATATAGA
* *
885114 GTTAATCTTTAAAAATCTTCTTCTCAAAAACCATTCGGCCAGAAAAGCTGATACTTGTGTGGAAG
260 GTTAATCTTTAAAAATCTTCTTCTCAAAAACCATTCGACCAGAAAAGCTGAAACTTGTGTGGAAG
885179 CATCCT
325 CATCCT
*
885185 CAGATAGTGTAGGTTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGG
1 CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGG
** ** * * * * *
885250 GTTTTGAATTTTTACATAGGAGTATATAGAGTTAATCTTCTAAAAAATCTTCTCAAAAGCCATTT
66 GGGTCAAATTTTTACATAGGAGTATATAGAG-AAAT-TTATTATAAATCTTCTCAAAAACCATTT
*
885315 GACCAGAAAAGCCGAAACTTGTGTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAAT
129 GACCAGAAAAGCCGAAACTTGTGTGGAAGCATCCTCAGATAGTGTAGATACAAGTTTGTTCAAAT
* *
885380 CATGGTCCCTGGGGGTAAGGTGGGGCCTCAAT-GGGGGGTCAAAGTTTTACATATAAGTATATAG
194 CATAGTCCCTGGGGGTAAGGTGGGGCCTCAATAGGGGGGTCAAAGTTTTACATAGAAGTATATAG
*
885444 AGTTAATCTTTAAAAATCTTCTTCTCAAAAACCATTTGACCAGAAAAGCTGAAACTTGTGTGGAA
259 AGTTAATCTTTAAAAATCTTCTTCTCAAAAACCATTCGACCAGAAAAGCTGAAACTTGTGTGGAA
885509 GCATCCT
324 GCATCCT
* * *
885516 CAGATGGTGTAGATTTATGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGG
1 CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGG
* * *
885581 GGGTCAAATTTTTACATAGGAATATAAAGAGAAATTTTATTTTTAAATCTTCT
66 GGGTCAAATTTTTACATAGGAGTATATAGAGAAA-TTTA-TTATAAATCTTCT
885634 ACACAGATCA
Statistics
Matches: 395, Mismatches: 42, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
323 86 0.22
325 2 0.01
330 4 0.01
331 196 0.50
333 107 0.27
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (330 bp):
CAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCACAATGGG
GGGTCAAATTTTTACATAGGAGTATATAGAGAAATTTATTATAAATCTTCTCAAAAACCATTTGA
CCAGAAAAGCCGAAACTTGTGTGGAAGCATCCTCAGATAGTGTAGATACAAGTTTGTTCAAATCA
TAGTCCCTGGGGGTAAGGTGGGGCCTCAATAGGGGGGTCAAAGTTTTACATAGAAGTATATAGAG
TTAATCTTTAAAAATCTTCTTCTCAAAAACCATTCGACCAGAAAAGCTGAAACTTGTGTGGAAGC
ATCCT
Found at i:890334 original size:130 final size:130
Alignment explanation
Indices: 890092--890334 Score: 279
Period size: 130 Copynumber: 1.9 Consensus size: 130
890082 ATTAAAAGCC
* * *
890092 AATTTTGCCTATCACAATCTTATATTCCTGTGCAGCATGTTCCATAGCTTCTATGAGACTTTTAA
1 AATTTTGCCAACCACAATCTTATACTCCTGTGCAGCATGTTCCATAGCTTCTATGAGACTTTTAA
* ** * *
890157 GGCTGTCTGATGAACAAATGTAGCTAACAAAGCATGGCACTCTTATCTTTTATAAAATGAACATT
66 GGCTGTCTGAGGAACAAATGTAGCTAACAAAGCACAGCACACATATCTTTTATAAAATGAACATT
* ** ** * *
890222 AATTTTGCCAACCACAATCTTATACTCCTGTGCCGTGTGTTCGGTGGCTTCTATGAGACTTTTCA
1 AATTTTGCCAACCACAATCTTATACTCCTGTGCAGCATGTTCCATAGCTTCTATGAGACTTTTAA
* * ** * * * *
890287 GGCTGTCTGCGGCACTCATGTAGCTGACGAAGTACAGCACAGATATCT
66 GGCTGTCTGAGGAACAAATGTAGCTAACAAAGCACAGCACACATATCT
890335 GTGACACCTC
Statistics
Matches: 90, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
130 90 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (130 bp):
AATTTTGCCAACCACAATCTTATACTCCTGTGCAGCATGTTCCATAGCTTCTATGAGACTTTTAA
GGCTGTCTGAGGAACAAATGTAGCTAACAAAGCACAGCACACATATCTTTTATAAAATGAACATT
Found at i:893737 original size:18 final size:18
Alignment explanation
Indices: 893698--893735 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
893688 TTTCATGCTG
893698 AAAT-TTATTTTTACGAA
1 AAATGTTATTTTTACGAA
893715 AAATGTTATTTTCTACGAA
1 AAATGTTATTTT-TACGAA
893734 AA
1 AA
893736 TGACAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
AAATGTTATTTTTACGAA
Found at i:896974 original size:21 final size:21
Alignment explanation
Indices: 896922--897007 Score: 118
Period size: 21 Copynumber: 4.0 Consensus size: 21
896912 AACAAAATTT
* *
896922 ATATAATAAAGCACTATCTTC
1 ATATAAAAAAGCACCATCTTC
*
896943 ACATAAAAAAAGCACCATCTTC
1 ATAT-AAAAAAGCACCATCTTC
*
896965 ATATAAAAAAGCACGATCTTC
1 ATATAAAAAAGCACCATCTTC
*
896986 ATATAATAAAGCACCATCTTC
1 ATATAAAAAAGCACCATCTTC
897007 A
1 A
897008 CATGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 39 0.68
22 18 0.32
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.26
Consensus pattern (21 bp):
ATATAAAAAAGCACCATCTTC
Found at i:896984 original size:43 final size:42
Alignment explanation
Indices: 896922--897007 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
896912 AACAAAATTT
* *
896922 ATATAATAAAGCACTATCTTCACATAAAAAAAGCACCATCTTC
1 ATATAAAAAAGCACGATCTTCACAT-AAAAAAGCACCATCTTC
* *
896965 ATATAAAAAAGCACGATCTTCATATAATAAAGCACCATCTTC
1 ATATAAAAAAGCACGATCTTCACATAAAAAAGCACCATCTTC
897007 A
1 A
897008 CATGAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 17 0.44
43 22 0.56
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.26
Consensus pattern (42 bp):
ATATAAAAAAGCACGATCTTCACATAAAAAAGCACCATCTTC
Found at i:897032 original size:42 final size:42
Alignment explanation
Indices: 896951--897065 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
896941 TCACATAAAA
* * *
896951 AAAGCACCATCTTCATAT-AAAAAAGCACGATCTTCATATAAT
1 AAAGCACCATCTTCATATGAAATAACCAC-AGCTTCATATAAT
*
896993 AAAGCACCATCTTCACATGAAATAACCACAGCATT-ATATAAT
1 AAAGCACCATCTTCATATGAAATAACCACAGC-TTCATATAAT
* *
897035 AAAGGCACCATCTTTATATGAAATAGCCACA
1 AAA-GCACCATCTTCATATGAAATAACCACA
897066 TATATATATG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (42 bp):
AAAGCACCATCTTCATATGAAATAACCACAGCTTCATATAAT
Found at i:897048 original size:64 final size:64
Alignment explanation
Indices: 896922--897053 Score: 160
Period size: 64 Copynumber: 2.1 Consensus size: 64
896912 AACAAAATTT
* * * *
896922 ATATAATAAAGCACTATCTTCACATAAAAAAAGCACCATCTTCATATAAAAAAGCACGATCTTC
1 ATATAATAAAGCACCATCTTCACATAAAAAAACCACCAGCTTCATATAAAAAAGCACCATCTTC
* * *
896986 ATATAATAAAGCACCATCTTCACATGAAATAACCA-CAGCATT-ATATAATAAAGGCACCATCTT
1 ATATAATAAAGCACCATCTTCACATAAAAAAACCACCAGC-TTCATATAA-AAAAGCACCATCTT
*
897049 T
64 C
897050 ATAT
1 ATAT
897054 GAAATAGCCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 9 0.16
64 49 0.84
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (64 bp):
ATATAATAAAGCACCATCTTCACATAAAAAAACCACCAGCTTCATATAAAAAAGCACCATCTTC
Found at i:897915 original size:2 final size:2
Alignment explanation
Indices: 897908--897959 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
897898 CACTGACCCC
897908 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
897950 CT CT CT CT CT
1 CT CT CT CT CT
897960 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:905232 original size:2 final size:2
Alignment explanation
Indices: 905225--905261 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
905215 NNNNNNNNNN
905225 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
905262 ATTGGTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:906407 original size:2 final size:2
Alignment explanation
Indices: 906400--906435 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
906390 TGAAACTATG
906400 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
906436 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:906458 original size:2 final size:2
Alignment explanation
Indices: 906451--906513 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
906441 NNNNNNNNNN
906451 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
906493 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
906514 AGAAAAAGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:907430 original size:14 final size:14
Alignment explanation
Indices: 907411--907437 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
907401 ATGCATTACT
907411 AGGAAAGTGAATAA
1 AGGAAAGTGAATAA
907425 AGGAAAGTGAATA
1 AGGAAAGTGAATA
907438 GGTTGTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (14 bp):
AGGAAAGTGAATAA
Found at i:937084 original size:77 final size:77
Alignment explanation
Indices: 936926--937084 Score: 221
Period size: 77 Copynumber: 2.1 Consensus size: 77
936916 TTTCTTATTT
* * * * *
936926 CTATTAATTGTGCAGTTGTGTGCCAAAAATTGTGTAGGCCTATAACAGTCACTTTTTCAAAATAA
1 CTATCAATTGTGAAGTTGTGTGCAAAAAATTGTGTAGGCCTATAAAAGTCACTTTATCAAAATAA
* *
936991 ATCAACTAGTTC
66 AGCAACTAGTTA
* *
937003 CTATCAATTGTGAAGTTGTGTGCAAAAAATTGTGTAGGCTTATAAAAGTCACTTTATCAAAATAT
1 CTATCAATTGTGAAGTTGTGTGCAAAAAATTGTGTAGGCCTATAAAAGTCACTTTATCAAAATAA
937068 AGCAACCT-GTTA
66 AGCAA-CTAGTTA
937080 CTATC
1 CTATC
937085 TGGGAAGAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (77 bp):
CTATCAATTGTGAAGTTGTGTGCAAAAAATTGTGTAGGCCTATAAAAGTCACTTTATCAAAATAA
AGCAACTAGTTA
Found at i:937901 original size:2 final size:2
Alignment explanation
Indices: 937894--937952 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
937884 TATAGAAGAC
*
937894 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
937936 GA GA GG GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
937953 GGGGTAGGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:946964 original size:4 final size:4
Alignment explanation
Indices: 946955--947010 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
946945 AGTTGCGTCT
* * * *
946955 ACAG ACAG ACGG ACAG ACGG ACAG ACGG ACAG ACAG ACAG ACGG ACAG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
*
947003 ACGG ACAG
1 ACAG ACAG
947011 GGTGAAACCA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.41, C:0.25, G:0.34, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:946971 original size:8 final size:8
Alignment explanation
Indices: 946958--947010 Score: 97
Period size: 8 Copynumber: 6.6 Consensus size: 8
946948 TGCGTCTACA
946958 GACAGACG
1 GACAGACG
946966 GACAGACG
1 GACAGACG
946974 GACAGACG
1 GACAGACG
*
946982 GACAGACA
1 GACAGACG
946990 GACAGACG
1 GACAGACG
946998 GACAGACG
1 GACAGACG
947006 GACAG
1 GACAG
947011 GGTGAAACCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.40, C:0.25, G:0.36, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:951734 original size:16 final size:17
Alignment explanation
Indices: 951713--951744 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
951703 ATGCGGGATG
951713 TACTAAAA-ACCTGAAA
1 TACTAAAAGACCTGAAA
951729 TACTAAAAGACCTGAA
1 TACTAAAAGACCTGAA
951745 TGTCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (17 bp):
TACTAAAAGACCTGAAA
Found at i:962384 original size:2 final size:2
Alignment explanation
Indices: 962379--962415 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
962369 TAAACACACA
*
962379 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
962416 CAGACAGACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:962453 original size:19 final size:20
Alignment explanation
Indices: 962429--962472 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
962419 ACAGACAGAC
962429 AGAGAA-AGGGATAAAGAA-G
1 AGAGAATAGGGA-AAAGAAGG
962448 AGAGAATAGGGAAAAGAAGG
1 AGAGAATAGGGAAAAGAAGG
962468 AGAGA
1 AGAGA
962473 TTATGAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.05
Consensus pattern (20 bp):
AGAGAATAGGGAAAAGAAGG
Found at i:970951 original size:2 final size:2
Alignment explanation
Indices: 970929--971041 Score: 104
Period size: 2 Copynumber: 57.5 Consensus size: 2
970919 CCCATTTTTT
* * * * *
970929 TC TC TT TC TC CC TC CC TC TC TC TC TC -C TC CC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * ** * * *
970970 TC TC TC TT TG TC GG TC TG TC TG TC TG TC TC T- TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
971011 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
971042 GTNNNNNNNN
Statistics
Matches: 88, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
1 2 0.02
2 86 0.98
ACGTcount: A:0.00, C:0.47, G:0.05, T:0.48
Consensus pattern (2 bp):
TC
Found at i:970959 original size:15 final size:15
Alignment explanation
Indices: 970929--970969 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
970919 CCCATTTTTT
*
970929 TCTCTTTCTCCCTCCC
1 TCTCTCTCT-CCTCCC
970945 TCTCTCTCTCCTCCC
1 TCTCTCTCTCCTCCC
*
970960 CCTCTCTCTC
1 TCTCTCTCTC
970970 TCTCTCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (15 bp):
TCTCTCTCTCCTCCC
Found at i:993757 original size:20 final size:20
Alignment explanation
Indices: 993705--993759 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
993695 TTTAAAAGAT
993705 TGATGGATGAACAGACAAAC
1 TGATGGATGAACAGACAAAC
** * * *
993725 TTTTGTATAAACAGACATAC
1 TGATGGATGAACAGACAAAC
993745 TGATGGATGAACAGA
1 TGATGGATGAACAGA
993760 ATAATGGATG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (20 bp):
TGATGGATGAACAGACAAAC
Found at i:1002270 original size:16 final size:16
Alignment explanation
Indices: 1002249--1002284 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1002239 ATGGTGCATA
1002249 TTTAATGCCTAAAAGT
1 TTTAATGCCTAAAAGT
1002265 TTTAATGCCTAAAAGT
1 TTTAATGCCTAAAAGT
1002281 TTTA
1 TTTA
1002285 CACATGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (16 bp):
TTTAATGCCTAAAAGT
Found at i:1003394 original size:2 final size:2
Alignment explanation
Indices: 1003387--1003413 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1003377 NNNNNNNNNN
1003387 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1003414 CTTAGTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1009092 original size:2 final size:2
Alignment explanation
Indices: 1009085--1009125 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1009075 TATGTAGCAA
1009085 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1009126 ATGTAAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1013094 original size:13 final size:13
Alignment explanation
Indices: 1013076--1013102 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1013066 CCATATATAT
1013076 ATAACAAGCACAA
1 ATAACAAGCACAA
1013089 ATAACAAGCACAA
1 ATAACAAGCACAA
1013102 A
1 A
1013103 CAAAACCTGT
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:0.63, C:0.22, G:0.07, T:0.07
Consensus pattern (13 bp):
ATAACAAGCACAA
Found at i:1013608 original size:26 final size:26
Alignment explanation
Indices: 1013568--1013620 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1013558 GTTTGACACA
* *
1013568 CACACACACACTGCATATTTCTAATT
1 CACACACACACTGCAGATTCCTAATT
*
1013594 CACACACACATTGCAGATTCCTAATT
1 CACACACACACTGCAGATTCCTAATT
1013620 C
1 C
1013621 TAATGCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (26 bp):
CACACACACACTGCAGATTCCTAATT
Found at i:1017255 original size:2 final size:2
Alignment explanation
Indices: 1017248--1017374 Score: 137
Period size: 2 Copynumber: 63.5 Consensus size: 2
1017238 AAAACATGTT
1017248 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * ** ** * * * * *
1017290 AC AC CC AC AC AC AC AC AC AC AC AC AC AG TG GG AG AG AG AG AG
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
1017332 AG AG AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1017374 A
1 A
1017375 GAGTAGGAGA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 118 1.00
ACGTcount: A:0.48, C:0.43, G:0.09, T:0.01
Consensus pattern (2 bp):
AC
Found at i:1017386 original size:2 final size:2
Alignment explanation
Indices: 1017381--1017418 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1017371 CACAGAGTAG
1017381 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1017419 AATATATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1019187 original size:1 final size:1
Alignment explanation
Indices: 1019181--1019210 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1019171 ATTTTATATC
1019181 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1019211 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1044115 original size:165 final size:164
Alignment explanation
Indices: 1043920--1044228 Score: 369
Period size: 165 Copynumber: 1.9 Consensus size: 164
1043910 GTTTATGGAA
* * * *
1043920 TTACTATGCATACATCCCTGGTTTATGTAGATTC-CTAATTTGTAAAATAGAGACCCCCGGACTA
1 TTACTATGCATACAACCCTGGATAATGTAGATTCGATAATTT-TAAAATAGAGACCCCCGGACTA
* *
1043984 ATACTAGGGCCCCAAGA-GGGATCAAAA-ATT-TGTA-AAGATATATATAGGTAACATGTTAAAA
65 ATACTAGGGACCCAAGATGGG-TCAAAAGATTATGTAGAAG-TATATAT-GG-AAAATGTT-AAA
1044045 AATCTTCTTCTT-GAGAACTTGGATGCTACAATTTGTAAAT
125 AATCTTCTT-TTCGAGAACTTGGATGCTACAATTTGTAAAT
** * * * *
1044085 TTACTATGCATACAACTTTGGATAATGTAGATTCGATAGTTTTAAAGTAGTGACCCCTGGACTAA
1 TTACTATGCATACAACCCTGGATAATGTAGATTCGATAATTTTAAAATAGAGACCCCCGGACTAA
* * *
1044150 TACTGGGGACCCAAGATGGGTTAAAAGTTTAGTGTAGAAGTATATATGGAAAATGTTAAAAATCT
66 TACTAGGGACCCAAGATGGGTCAAAAGATTA-TGTAGAAGTATATATGGAAAATGTTAAAAATCT
1044215 TCTTTTCGAGAACT
130 TCTTTTCGAGAACT
1044229 ACAATGTTTC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
164 2 0.02
165 87 0.71
166 17 0.14
167 2 0.02
168 11 0.09
169 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (164 bp):
TTACTATGCATACAACCCTGGATAATGTAGATTCGATAATTTTAAAATAGAGACCCCCGGACTAA
TACTAGGGACCCAAGATGGGTCAAAAGATTATGTAGAAGTATATATGGAAAATGTTAAAAATCTT
CTTTTCGAGAACTTGGATGCTACAATTTGTAAAT
Found at i:1044281 original size:165 final size:166
Alignment explanation
Indices: 1044110--1044411 Score: 355
Period size: 165 Copynumber: 1.8 Consensus size: 166
1044100 CTTTGGATAA
* * * *
1044110 TGTAGATTCGATAGTT-TTAAAGTAGTGACCCCTGGA-CTAATACTGGGGACC-CAAGATGG-GT
1 TGTAGATTCGA-AATTATAAAAGCAGTGA-CCCTCGATCTAATACTGGGG-CCACAAGA-GGTGT
* *** * * * *
1044171 TAAAAGTTTAGTGTAGAAGTATATATGGAAAATG-TTAAAAATCTTCTTT-TCGAGAACTACAAT
62 TAAAAGTTAAACATAGAAATATAGAGGGAAAATGTTTAAAAATCTT-TTTCTAGAGAACTACAAT
* *
1044234 GTTTCAATTTGTCAGATAACTACGTAAGCATCCTCAAATTG
126 GCTTCAACTTGTCAGATAACTACGTAAGCATCCTCAAATTG
* * * *
1044275 TGTAGATTCGAAATTATAAAAGCCGTGACCCTCGATCTAATATTGGGGCCACAGGAGGTGTTCAA
1 TGTAGATTCGAAATTATAAAAGCAGTGACCCTCGATCTAATACTGGGGCCACAAGAGGTGTTAAA
1044340 AGTTAAACATAGAAATATAGAGGGAAAATGTTTAAAAATCTTTTTCTAGAGAACTACAATGCTTC
66 AGTTAAACATAGAAATATAGAGGGAAAATGTTTAAAAATCTTTTTCTAGAGAACTACAATGCTTC
1044405 AACTTGT
131 AACTTGT
1044412 GAGACATTGT
Statistics
Matches: 113, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
164 13 0.12
165 66 0.58
166 34 0.30
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (166 bp):
TGTAGATTCGAAATTATAAAAGCAGTGACCCTCGATCTAATACTGGGGCCACAAGAGGTGTTAAA
AGTTAAACATAGAAATATAGAGGGAAAATGTTTAAAAATCTTTTTCTAGAGAACTACAATGCTTC
AACTTGTCAGATAACTACGTAAGCATCCTCAAATTG
Found at i:1045482 original size:21 final size:21
Alignment explanation
Indices: 1045448--1045527 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
1045438 AATTTAATGC
* *
1045448 TATGCTATGGTATGCGATTT-
1 TATGCTATGCTATGAGATTTG
*
1045468 TAATGATATGCTATGAGATTTG
1 T-ATGCTATGCTATGAGATTTG
1045490 TATGCTATGCTATGAGATTTG
1 TATGCTATGCTATGAGATTTG
1045511 TATGCTATGCTATGAGA
1 TATGCTATGCTATGAGA
1045528 AATTGAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
TATGCTATGCTATGAGATTTG
Found at i:1045569 original size:10 final size:10
Alignment explanation
Indices: 1045551--1045585 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1045541 GGCTTAATGA
*
1045551 TATGGTATGC
1 TATGATATGC
1045561 TATGATATGC
1 TATGATATGC
*
1045571 TATGGTATGC
1 TATGATATGC
1045581 TATGA
1 TATGA
1045586 GATTTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (10 bp):
TATGATATGC
Found at i:1045869 original size:26 final size:21
Alignment explanation
Indices: 1045789--1045864 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
1045779 ATGAGATTGT
* *
1045789 ATGCTATGGTATGAGATTCCA
1 ATGCTATGCTATGAGATTTCA
1045810 ATGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTTCA
1045831 ATGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTTCA
1045852 ATGCTATGCTATG
1 ATGCTATGCTATG
1045865 CTATGGTGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTTCA
Found at i:1060881 original size:14 final size:14
Alignment explanation
Indices: 1060862--1060906 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
1060852 AGCCCTATCC
1060862 TATCCTGTATCCAG
1 TATCCTGTATCCAG
1060876 TATCCTGTATCCTA-
1 TATCCTGTATCC-AG
1060890 TATCCTGTATCCAG
1 TATCCTGTATCCAG
1060904 TAT
1 TAT
1060907 TCTATTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (14 bp):
TATCCTGTATCCAG
Done.