Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 2 of 24
Found at i:166746 original size:107 final size:105
Alignment explanation
Indices: 166387--166778 Score: 296
Period size: 107 Copynumber: 3.7 Consensus size: 105
166377 CCCTCAAAAA
* * * * **
166387 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTT-GGAATAAAATCGGGGTTGGAG
* *
166452 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * * * *
166494 TAACGAGGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGG-AATAAAATCGGGGTTGGA
* * ** * ** **
166559 GTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
64 GTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * *
166596 AAAACCGGGATTAGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCG-ATAAAATCGGGGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTT-G-GAATAAAATCGGGGTT
166660 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
61 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
166705 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTT
1 TAACGGGGTTGGAGTATCCCCGATTATGAA-AAATT--AG-TATTTTGG-AATAAAATCGGGGTT
*
166770 AGAGTATCC
61 GGAGTATCC
166779 TCGATTATAG
Statistics
Matches: 214, Mismatches: 49, Indels: 41
0.70 0.16 0.13
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 48 0.22
105 16 0.07
106 18 0.08
107 63 0.29
108 32 0.15
109 6 0.03
110 26 0.12
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAATAAAATCGGGGTTGGAGT
ATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:166775 original size:55 final size:51
Alignment explanation
Indices: 166716--166843 Score: 132
Period size: 51 Copynumber: 2.4 Consensus size: 51
166706 AACGGGGTTG
* * *
166716 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTG-AGAAATTAGTG---CTTTGAAAATAAAATCGGAGTTA
* * *
166771 GAGTATCCTCGATTAT-AGAAAATTAGTGCTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGCTTTGAAAATAAAATCGGAGTTA
*
166822 GAATATCCCCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
166844 TTGAGAAACT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
51 33 0.54
52 2 0.03
53 4 0.07
54 8 0.13
55 14 0.23
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGCTTTGAAAATAAAATCGGAGTTA
Found at i:169156 original size:20 final size:20
Alignment explanation
Indices: 169131--169294 Score: 100
Period size: 20 Copynumber: 7.8 Consensus size: 20
169121 AAAACGCTTG
*
169131 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
* *
169151 AATGTATCGATACACTGAGT
1 AATGTATCGATACAATGAGA
* *
169171 AATGTATCAATACAATGAGC
1 AATGTATCGATACAATGAGA
169191 AATGTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
* * * *
169211 AATGTATCAATATATCTAGGTAAACCCA
1 AATGTATC--GATA-C-A-AT-GA--GA
*
169239 GAATGTATCGATACAATGAGC
1 -AATGTATCGATACAATGAGA
169260 AATGTATCGATACAATGA-A
1 AATGTATCGATACAATGAGA
*
169279 CAATGTATCGTTACAA
1 -AATGTATCGATACAA
169295 ATTGTGAAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 26
0.73 0.11 0.17
Matches are distributed among these distances:
19 1 0.01
20 89 0.78
21 1 0.01
22 3 0.03
23 2 0.02
24 2 0.02
25 3 0.03
26 1 0.01
27 3 0.03
28 1 0.01
29 8 0.07
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:170214 original size:59 final size:59
Alignment explanation
Indices: 170049--170793 Score: 886
Period size: 59 Copynumber: 12.9 Consensus size: 59
170039 ATAAAGTGTA
* * * * *
170049 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
170104 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
170163 TCCTGCACTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
170222 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
170281 T-CTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCT-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
170340 TCCCGCTCTTTGAGGATTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** * *
170399 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** *
170454 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
170509 TCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * * *
170570 TCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
170629 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
170688 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
170742 TCCTGCTCTCTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
170794 GTGTCCTGCT
Statistics
Matches: 618, Mismatches: 52, Indels: 38
0.87 0.07 0.05
Matches are distributed among these distances:
54 21 0.03
55 167 0.27
57 6 0.01
58 27 0.04
59 322 0.52
60 54 0.09
61 21 0.03
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:173242 original size:21 final size:22
Alignment explanation
Indices: 173213--173258 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
173203 TGTTCATACA
** *
173213 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
173235 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
173256 AGT
1 AGT
173259 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:173638 original size:2 final size:2
Alignment explanation
Indices: 173631--173668 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
173621 TATAGGCATG
173631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173669 TCGATTTGTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:177112 original size:18 final size:18
Alignment explanation
Indices: 177086--177120 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
177076 TATTTTCATG
*
177086 ATTTAAAGACCATTTAGC
1 ATTTAAAGAACATTTAGC
*
177104 ATTTTAAGAACATTTAG
1 ATTTAAAGAACATTTAG
177121 AATAGTTTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
ATTTAAAGAACATTTAGC
Found at i:179337 original size:2 final size:2
Alignment explanation
Indices: 179332--179409 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
179322 TGTGAGTGTG
*
179332 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
179374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
179410 AACTAATAGA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:184242 original size:51 final size:51
Alignment explanation
Indices: 184186--184332 Score: 240
Period size: 51 Copynumber: 2.9 Consensus size: 51
184176 TTTTAACTAG
*
184186 ATGTATCGATACATTGAAAAATGTATTGATACATCTAGGTAAAAAGACAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAAA
* * * * *
184237 ATGTATCGATACATTCAAAAATATATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAAA
184288 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
184333 TGTGACTTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 87 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAAA
Found at i:185872 original size:114 final size:113
Alignment explanation
Indices: 185564--185884 Score: 353
Period size: 113 Copynumber: 2.8 Consensus size: 113
185554 TATTTAATTG
* * * * *
185564 AATAACAATCATCC-AAAAATCATGATATTTTTATTAT-AT--TTTACCTAAATTACAACAGTTA
1 AATAACAATTATCCTAAAAATCATAATAATTTT-TTATCATCGTTCA-CTAGATTACAACAGTTA
* * * * **
185625 ATAAAAGATAAAATTATAAATCTATTAACTTTATTATTTTTAAAATTTAA
64 ATAAAAGATAAAATTATAAACCTATCAATTTTATTATTATTAAAAACTAA
* * * * * ** * *
185675 AATAACAATTTTCCTAAAATTTATAATAATTTTTTATTATCTTTGTCTAGATTATAACAATTAAT
1 AATAACAATTATCCTAAAAATCATAATAATTTTTTATCATCGTTCACTAGATTACAACAGTTAAT
*
185740 AAAAAATAAAATTATAAACCTATCAATTTTATTATTATTAAAAACTAA
66 AAAAGATAAAATTATAAACCTATCAATTTTATTATTATTAAAAACTAA
* * * *
185788 AATAATAATTATCTTAAAAATCATTATAATTTTTTATCATCGTTCACATAGATTACAACTGTTAA
1 AATAACAATTATCCTAAAAATCATAATAATTTTTTATCATCGTTCAC-TAGATTACAACAGTTAA
*
185853 TAAAAGATAAAATTATAAACCTCTCAATTTTA
65 TAAAAGATAAAATTATAAACCTATCAATTTTA
185885 GCCTACAACT
Statistics
Matches: 172, Mismatches: 33, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
111 16 0.09
112 16 0.09
113 94 0.55
114 46 0.27
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (113 bp):
AATAACAATTATCCTAAAAATCATAATAATTTTTTATCATCGTTCACTAGATTACAACAGTTAAT
AAAAGATAAAATTATAAACCTATCAATTTTATTATTATTAAAAACTAA
Found at i:188908 original size:96 final size:96
Alignment explanation
Indices: 188703--188910 Score: 269
Period size: 97 Copynumber: 2.2 Consensus size: 96
188693 ACATTACAAT
*
188703 CTAAATTAAGAAATTTTAATTGAAAACCAATCAAGAGTAATAAAAATCAAAACAACCAATATTTC
1 CTAAATTAAGAAGTTTTAATTGAAAACCAATCAAGAG-AATAAAAATCAAAACAACCAATATTTC
*
188768 ATTTTGCATAATTTTTTTATGGATAAAAAAAA
65 ATTTTGCATAATTTTTTTATGGACAAAAAAAA
** * *
188800 CTAAATTAAGAAGTTTTAATTGAAAATTAATCAAGTA-AAT-AAAGTC-AAATAACCAATATTTC
1 CTAAATTAAGAAGTTTTAATTGAAAACCAATCAAG-AGAATAAAAATCAAAACAACCAATATTTC
* * *
188862 ATTTTTCATACTTTTTTTCATGGACCCAAAAAAA
65 ATTTTGCATAATTTTTTT-ATGGA-CAAAAAAAA
*
188896 CTATATTAAGAAGTT
1 CTAAATTAAGAAGTT
188911 AAAAAAACTA
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
94 31 0.32
95 10 0.10
96 24 0.24
97 32 0.33
98 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (96 bp):
CTAAATTAAGAAGTTTTAATTGAAAACCAATCAAGAGAATAAAAATCAAAACAACCAATATTTCA
TTTTGCATAATTTTTTTATGGACAAAAAAAA
Found at i:188931 original size:96 final size:94
Alignment explanation
Indices: 188756--188931 Score: 221
Period size: 94 Copynumber: 1.9 Consensus size: 94
188746 AAATCAAAAC
* * **
188756 AACCAATATTTCATTTTGCATAATTTTTTTATGGATAAAAAAAACTAAATTAAGAAGTTTTAATT
1 AACCAATATTTCATTTTGCATAATTTTTTTATGGACAAAAAAAACTAAATTAAGAAGTTTAAAAA
*
188821 GAAAATTAATCAAGTAAATAAAGTCAAAT
66 AAAAATTAATCAAGTAAATAAAGTCAAAT
* * * *
188850 AACCAATATTTCATTTTTCATACTTTTTTTCATGGACCCAAAAAAACTATATTAAGAAG-TTAAA
1 AACCAATATTTCATTTTGCATAATTTTTTT-ATGGA-CAAAAAAAACTAAATTAAGAAGTTTAAA
188914 AAAACTAAATTAA-CAAGT
64 AAAA--AAATTAATCAAGT
188932 TTTAATTGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
94 28 0.41
95 10 0.14
96 24 0.35
97 7 0.10
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (94 bp):
AACCAATATTTCATTTTGCATAATTTTTTTATGGACAAAAAAAACTAAATTAAGAAGTTTAAAAA
AAAAATTAATCAAGTAAATAAAGTCAAAT
Found at i:188936 original size:24 final size:22
Alignment explanation
Indices: 188889--188932 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
188879 TCATGGACCC
* *
188889 AAAAAAACTATATTAAGAAGTT
1 AAAAAAACTAAATTAACAAGTT
188911 AAAAAAACTAAATTAACAAGTT
1 AAAAAAACTAAATTAACAAGTT
188933 TTAATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (22 bp):
AAAAAAACTAAATTAACAAGTT
Found at i:190269 original size:34 final size:34
Alignment explanation
Indices: 190223--190437 Score: 238
Period size: 34 Copynumber: 6.4 Consensus size: 34
190213 GTAAAAACCA
**
190223 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
190257 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * * *
190291 CCATTTAATCAACAATGGTAAGCTACTAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
190325 TCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
190359 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
190393 CTATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
190426 CCATTTAATCAA
1 CCATTTAATCAA
190438 TAATTCTCCC
Statistics
Matches: 151, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
33 15 0.10
34 131 0.87
35 5 0.03
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:190365 original size:102 final size:102
Alignment explanation
Indices: 190224--190423 Score: 337
Period size: 102 Copynumber: 2.0 Consensus size: 102
190214 TAAAAACCAC
* *
190224 CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
*
190289 ACCCATTTAATCAACAATGGTAAGCTACTAAATTTTT
66 ACCCATTTAATCAACAATGGTAAACTACTAAATTTTT
** *
190326 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
1 CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
*
190391 ACCTATTTAATCAACAATGGTAAACTACTAAAT
66 ACCCATTTAATCAACAATGGTAAACTACTAAAT
190424 CACCATTTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (102 bp):
CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
ACCCATTTAATCAACAATGGTAAACTACTAAATTTTT
Found at i:201739 original size:38 final size:37
Alignment explanation
Indices: 201688--201761 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
201678 TTGATAAAAA
201688 TTTTGAAAAATATATTTTA-AAAACTTTGAATGAATTAG
1 TTTTGAAAAATATATTTTATAAAA-TTT-AATGAATTAG
* * *
201726 TTTTTAAATATATATTTTATAAAATTTAATTAATTA
1 TTTTGAAAAATATATTTTATAAAATTTAATGAATTA
201762 AAATATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 8 0.25
38 20 0.62
39 4 0.12
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (37 bp):
TTTTGAAAAATATATTTTATAAAATTTAATGAATTAG
Found at i:201860 original size:18 final size:18
Alignment explanation
Indices: 201837--201874 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
201827 TTAATTGGAA
*
201837 AAATTTTAATCAAAATTT
1 AAATTTTAATCAAAAATT
*
201855 AAATTTTAATTAAAAATT
1 AAATTTTAATCAAAAATT
201873 AA
1 AA
201875 CAAAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTTAATCAAAAATT
Found at i:204678 original size:310 final size:309
Alignment explanation
Indices: 204087--204860 Score: 848
Period size: 310 Copynumber: 2.5 Consensus size: 309
204077 AAAATGCCCA
* * * * *
204087 TAGGGTATACTTTCGATGTAGAAGTACCTGATACCCCTAAAAGACTTAAAAATGATTATAGATA-
1 TAGGGGATACTTTCGACGTAGAAGTACCCGATACCCCTAAAAGACTTAAAAAGGATTATA-AAAG
* * * * * * *
204151 GGATGAACATATCCTAAATACCCACATTCGACATAAAAGCGGACCTAGTGATATCTTAGACTCGG
65 GGATGAACCTATCCTAAATA-CCACCTTCGACATAAAAACGGACCTGGTGAAACCTAAGACTCGG
* * * * *
204216 TTCTAGAAAATTACGAAAATGCTCCT-ATGGATGTACCTTCGACAAGAAAGTATCCCAGTAAACC
129 TTCTAAAAAATTACAAAAATAC-CCTAACGGATGTACCTTCAACAAGAAAGTATCCCAGTAAACC
* *
204280 TAAAAGACTTAAAAAGGATATAGCTAGGGTGAACTTATCCTAAATATTGACCTTCAGCATAAAAA
193 TAAAAGACTTAAAAAGGATATAGATAGGGTGAACCTATCCTAAATATTGACCTTCAGCATAAAAA
* * * * *
204345 CAAACTCGGTGATAACTTAGGACTTAGTTCTAGAAAATTACAAAGATACCTC
258 CAAACTCGGTGACAACCTAGGACTCAGCTCTAGAAAATTACAAAAATACCTC
* * *
204397 TAGGGGATACTTTCAACGTAGAAGTACCCGATACCCCTAAAGGACTTAAAAAGGATTTTAAAAGG
1 TAGGGGATACTTTCGACGTAGAAGTACCCGATACCCCTAAAAGACTTAAAAAGGATTATAAAAGG
* * *** *
204462 GATGAACCTATCCTAAATATCCACCTTTGACGTAAAAATAAACCTGGTGACAACCTAAGACTCAG
66 GATGAACCTATCCTAAATA-CCACCTTCGACATAAAAACGGACCTGGTGA-AACCTAAGACTCGG
* * * * *
204527 TTCTAAAAAATTACAAAAATACCACTAACGG-T-TACTTTCAATATGAAAGTATCCGA-TAACCC
129 TTCTAAAAAATTACAAAAATACC-CTAACGGATGTACCTTCAACAAGAAAGTATCCCAGTAAACC
*
204589 TAAAAGACTT-AAAAGAGATTATAGAT-GGGATGAACCTATCCTAAATATCT-ACCTTCGGCATA
193 TAAAAGACTTAAAAAG-GA-TATAGATAGGG-TGAACCTATCCTAAATAT-TGACCTTCAGCATA
* ** *
204651 AAAGCGGA-TCCGGTGACAACCTAGGACTCAGCTCTAGAAAATTACAAAAATGCCTC
254 AAAACAAACT-CGGTGACAACCTAGGACTCAGCTCTAGAAAATTACAAAAATACCTC
* * * * * * *
204707 TAGGGGATACCTTCGACATAAAAGTACCCGATACCCTTAAATGACTT-AAAAGAGATTATAGATG
1 TAGGGGATACTTTCGACGTAGAAGTACCCGATACCCCTAAAAGACTTAAAAAG-GATTATAAAAG
* * * * *
204771 GGATGAACCTATCATAAATACCTATCTTCAACATAAAAACGGACCCGATGATAACCTAAGACTCG
65 GGATGAACCTATCCTAAATACC-ACCTTCGACATAAAAACGGACCTGGTGA-AACCTAAGACTCG
*
204836 GTTCTAAAAAATTATAAAAATACCC
128 GTTCTAAAAAATTACAAAAATACCC
204861 CTAAAGAGTA
Statistics
Matches: 387, Mismatches: 66, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
308 5 0.01
309 31 0.08
310 315 0.81
311 33 0.09
312 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (309 bp):
TAGGGGATACTTTCGACGTAGAAGTACCCGATACCCCTAAAAGACTTAAAAAGGATTATAAAAGG
GATGAACCTATCCTAAATACCACCTTCGACATAAAAACGGACCTGGTGAAACCTAAGACTCGGTT
CTAAAAAATTACAAAAATACCCTAACGGATGTACCTTCAACAAGAAAGTATCCCAGTAAACCTAA
AAGACTTAAAAAGGATATAGATAGGGTGAACCTATCCTAAATATTGACCTTCAGCATAAAAACAA
ACTCGGTGACAACCTAGGACTCAGCTCTAGAAAATTACAAAAATACCTC
Found at i:204873 original size:155 final size:155
Alignment explanation
Indices: 204108--204874 Score: 646
Period size: 155 Copynumber: 4.9 Consensus size: 155
204098 TTCGATGTAG
* * * *
204108 AAGTACCTGATACCCCTAAAAGACTTAAAAATGATTATAGATAGGATGAACATATCCTAAATACC
1 AAGTACCCGATA-CCCTAAAAGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
* * * ** * * * * *
204173 CACATTCGACATAAAAGCGGACCTAGTGAT-ATCTTAGACTCGGTTCTAGAAAATTACGAAAATG
65 TACCTTCGACATAAAAACGGACCCGGTGATAACCTAAGACTCAGTTCTAGAAAATTACAAAAATA
* * *
204237 CTCCTATGGATG-TACCTTCGACA-AGA
130 CCCCTAAGGA-GATACCTTCAACATA-A
* * *
204263 AAGTATCCC-AGTAAACCTAAAAGACTTAAAAAGGA-TATAGCTAGGG-TGAACTTATCCTAAAT
1 AAGTA-CCCGA-T-ACCCTAAAAGACTTAAAAAGGATTATAGAT-GGGATGAACCTATCCTAAAT
* ** * * * *
204325 A-TTGACCTTC-AGCATAAAAACAAACTCGGTGATAACTTAGGACTTAGTTCTAGAAAATTACAA
62 ACCT-ACCTTCGA-CATAAAAACGGACCCGGTGATAACCTAAGACTCAGTTCTAGAAAATTACAA
* * * * * *
204388 AGATACCTCT-AGGGGATACTTTCAACGTAG
125 AAATACCCCTAAGGAGATACCTTCAACATAA
* * * *
204418 AAGTACCCGATACCCCTAAAGGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATC
1 AAGTACCCGATA-CCCTAAAAGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATA-C
* * *** * * *
204483 C-ACCTTTGACGTAAAAATAAACCTGGTGACAACCTAAGACTCAGTTCTAAAAAATTACAAAAAT
64 CTACCTTCGACATAAAAACGGACCCGGTGATAACCTAAGACTCAGTTCTAGAAAATTACAAAAAT
* * * * * *
204547 ACCACTAACG-GTTACTTTCAATATGA
129 ACCCCTAAGGAGATACCTTCAACATAA
* *
204573 AAGTATCCGATAACCCTAAAAGACTT-AAAAGAGATTATAGATGGGATGAACCTATCCTAAATAT
1 AAGTACCCGAT-ACCCTAAAAGACTTAAAAAG-GATTATAGATGGGATGAACCTATCCTAAATAC
* * * * * *
204637 CTACCTTCGGCATAAAAGCGGATCCGGTGACAACCTAGGACTCAGCTCTAGAAAATTACAAAAAT
64 CTACCTTCGACATAAAAACGGACCCGGTGATAACCTAAGACTCAGTTCTAGAAAATTACAAAAAT
* * * *
204702 GCCTCT-AGGGGATACCTTCGACATAA
129 ACCCCTAAGGAGATACCTTCAACATAA
* *
204728 AAGTACCCGATACCCTTAAATGACTT-AAAAGAGATTATAGATGGGATGAACCTATCATAAATAC
1 AAGTACCCGATACCC-TAAAAGACTTAAAAAG-GATTATAGATGGGATGAACCTATCCTAAATAC
* * * * * *
204792 CTATCTTCAACATAAAAACGGACCCGATGATAACCTAAGACTCGGTTCTAAAAAATTATAAAAAT
64 CTACCTTCGACATAAAAACGGACCCGGTGATAACCTAAGACTCAGTTCTAGAAAATTACAAAAAT
*
204857 ACCCCTAAAGAG-TACCTT
129 ACCCCTAAGGAGATACCTT
204875 TGATGTAGAA
Statistics
Matches: 485, Mismatches: 104, Indels: 46
0.76 0.16 0.07
Matches are distributed among these distances:
153 1 0.00
154 40 0.08
155 383 0.79
156 60 0.12
157 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (155 bp):
AAGTACCCGATACCCTAAAAGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCT
ACCTTCGACATAAAAACGGACCCGGTGATAACCTAAGACTCAGTTCTAGAAAATTACAAAAATAC
CCCTAAGGAGATACCTTCAACATAA
Found at i:206998 original size:164 final size:162
Alignment explanation
Indices: 206677--207384 Score: 607
Period size: 164 Copynumber: 4.3 Consensus size: 162
206667 AAATAAATTT
* * * * * * * * **
206677 AATTTTGCAAAACTGATTTAATAGGAATTTAATAAAAATATTAG-TTATTTTTTAAAAATTTTAA
1 AATTTT-CAAAAATGATTTAATATGAATTAAATAATAATGTTTGATGA-ATTTTAAAAATTAAAA
* * * * * *
206741 ACAAAAAAAAGTCCTCCGAAAACCTTTACGGAATAGAAAATTCAGT-TTTTCGAAAACATGA-AA
64 ACCAAGAAAA-TCCCCCGAAAACATTTATGGAATAGAAAACTCAGTATTTT-GAAAACA-GAGAA
*
206804 A-TTTCAAAGAAAAAATTTAAAACTCATGAAAATGAATG
126 ATTTTC-AA-AAAAAATTCAAAACTCATGAAAATGAATG
* *
206842 AATATCTCAAAAATGATTTAATATGAATTAAATAATAATGTTTGATGAATTTTAAAAATTAAATA
1 AAT-TTTCAAAAATGATTTAATATGAATTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAA
* * * *
206907 CTAAGAAAAATCCACTCGAAAACATTTATGGAATATAAAACTCTGTATTTTGAAAACAGAGAAAT
65 CCAAG-AAAATCC-CCCGAAAACATTTATGGAATAGAAAACTCAGTATTTTGAAAACAGAGAAAT
206972 TTTC-AAAAAAATTCAAAACTCATGAAAATGAATG
128 TTTCAAAAAAAATTCAAAACTCATGAAAATGAATG
* * * *
207006 AATTTTTGAAAACTGATTTAAAATGAATTAAATAATAATGTTTTATGAATTTTAAAAATTAAAAA
1 AA-TTTTCAAAAATGATTTAATATGAATTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAA
* * * *
207071 CCAAGAAAATCCCCCGAAAATATTTATGGAGTAGAAAACTCCGTATTTCGAAAACA-AGAAAATT
65 CCAAGAAAATCCCCCGAAAACATTTATGGAATAGAAAACTCAGTATTTTGAAAACAGAG-AAATT
* *
207135 TTCGAAAAAAATTCAAAACTCATGAAAATGAATA
129 TTCAAAAAAAATTCAAAACTCATGAAAATGAATG
* * * * * * *
207169 AATTTTTAAAATTTAATTTAATTTGAATTAAATAATAATATTTGATAAATTTTAAAAATTTTAAA
1 AATTTTCAAAA-ATGATTTAATATGAATTAAATAATAATGTTTGATGAATTTTAAAAA-TTAAAA
* * * * * * * *
207234 TCTATGAAAATCCTCCCGAAAAAAATTTACGGAGA-AG-AAACTCCGTATTTTAAAAATAAGAGA
64 ACCAAGAAAATCC-CCCG-AAAACATTTATGGA-ATAGAAAACTCAGTATTTTGAAAA-CAGAGA
* * *
207297 AA-TTCCAAAAGAAAATT-AATAAGTCAT-AAAAT-AA-A
125 AATTTTCAAAA-AAAATTCAA-AACTCATGAAAATGAATG
** * * * * *
207332 AAAATTCAAAAATGATTTTATAGTG-ATTAAATGATAATATTTAAAGAATTTTA
1 AATTTTCAAAAATGATTTAATA-TGAATTAAATAATAATGTTTGATGAATTTTA
207385 GGGCTTGAAA
Statistics
Matches: 455, Mismatches: 68, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
161 2 0.00
162 85 0.19
163 88 0.19
164 106 0.23
165 91 0.20
166 73 0.16
167 10 0.02
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.32
Consensus pattern (162 bp):
AATTTTCAAAAATGATTTAATATGAATTAAATAATAATGTTTGATGAATTTTAAAAATTAAAAAC
CAAGAAAATCCCCCGAAAACATTTATGGAATAGAAAACTCAGTATTTTGAAAACAGAGAAATTTT
CAAAAAAAATTCAAAACTCATGAAAATGAATG
Found at i:207198 original size:163 final size:162
Alignment explanation
Indices: 206756--207283 Score: 625
Period size: 164 Copynumber: 3.2 Consensus size: 162
206746 AAAAAGTCCT
* * * * *
206756 CCGAAAACCTTTACGGAATAGAAAATTCAGTTTTTCGAAAACATGAAAA-TTTCAAAGAAAAAAT
1 CCGAAAACATTTACGGAATAGAAAACTCCGTATTTCGAAAACAAGAAAATTTTC--A-AAAAAAT
* * *
206820 TTAAAACTCATGAAAATGAATGAATATCTCAAAAATGATTTAATATGAATTAAATAATAATGTTT
63 TCAAAACTCATGAAAATGAATGAAT-TTTTAAAAATGATTTAATATGAATTAAATAATAATGTTT
*
206885 GATGAATTTTAAAAATTAAATACTAAGAAAAATCCAC
127 GATGAATTTTAAAAATTAAAAACTAAG-AAAATCCAC
* * * * *
206922 TCGAAAACATTTATGGAATATAAAACTCTGTATTTTGAAAAC-AGAGAAATTTTCAAAAAAATTC
1 CCGAAAACATTTACGGAATAGAAAACTCCGTATTTCGAAAACAAGA-AAATTTTCAAAAAAATTC
* * *
206986 AAAACTCATGAAAATGAATGAATTTTTGAAAACTGATTTAAAATGAATTAAATAATAATGTTTTA
65 AAAACTCATGAAAATGAATGAATTTTT-AAAAATGATTTAATATGAATTAAATAATAATGTTTGA
*
207051 TGAATTTTAAAAATTAAAAACCAAGAAAATCC-C
129 TGAATTTTAAAAATTAAAAACTAAGAAAATCCAC
* * *
207084 CCGAAAATATTTATGGAGTAGAAAACTCCGTATTTCGAAAACAAGAAAATTTTCGAAAAAAATTC
1 CCGAAAACATTTACGGAATAGAAAACTCCGTATTTCGAAAACAAGAAAATTTTC-AAAAAAATTC
* * * * *
207149 AAAACTCATGAAAATGAATAAATTTTTAAAATTTAATTTAATTTGAATTAAATAATAATATTTGA
65 AAAACTCATGAAAATGAATGAATTTTTAAAA-ATGATTTAATATGAATTAAATAATAATGTTTGA
* * * * *
207214 TAAATTTTAAAAATTTTAAATCTATGAAAATCCTC
129 TGAATTTTAAAAA-TTAAAAACTAAGAAAATCCAC
*
207249 CCGAAAAAAATTTACGGAGA-AG-AAACTCCGTATTT
1 CCG-AAAACATTTACGGA-ATAGAAAACTCCGTATTT
207284 TAAAAATAAG
Statistics
Matches: 314, Mismatches: 38, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
162 49 0.16
163 87 0.28
164 103 0.33
165 20 0.06
166 51 0.16
167 4 0.01
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (162 bp):
CCGAAAACATTTACGGAATAGAAAACTCCGTATTTCGAAAACAAGAAAATTTTCAAAAAAATTCA
AAACTCATGAAAATGAATGAATTTTTAAAAATGATTTAATATGAATTAAATAATAATGTTTGATG
AATTTTAAAAATTAAAAACTAAGAAAATCCAC
Found at i:208596 original size:32 final size:30
Alignment explanation
Indices: 208560--208618 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
208550 GAAATTAAAT
208560 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
208592 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
208619 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:208903 original size:20 final size:20
Alignment explanation
Indices: 208878--208930 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
208868 TACAAGCCAA
208878 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
*
208898 TGTATCGATGCAATTTTTTG
1 TGTATCGATACAATTTTTTG
208918 TGTATCGATACAA
1 TGTATCGATACAA
208931 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATTTTTTG
Found at i:211016 original size:21 final size:20
Alignment explanation
Indices: 210987--211029 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
210977 GACTAGTGTG
*
210987 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
* *
211008 GGGAGTGCCGGTCGTGACCT
1 GGGACTGCCGGTCGCGACCT
211028 GG
1 GG
211030 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:211489 original size:13 final size:13
Alignment explanation
Indices: 211471--211508 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
211461 ATAATCCCCC
211471 TGTATCGATACAG
1 TGTATCGATACAG
*
211484 TGTATCGATACAT
1 TGTATCGATACAG
211497 TGTATCGATACA
1 TGTATCGATACA
211509 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:213599 original size:15 final size:15
Alignment explanation
Indices: 213579--213609 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
213569 ATTTCGTTTG
*
213579 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
213594 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
213609 G
1 G
213610 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:215440 original size:21 final size:21
Alignment explanation
Indices: 215411--215455 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
215401 AAGTTTTTAT
*
215411 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
215431 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
215453 TTT
1 TTT
215456 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:217373 original size:32 final size:30
Alignment explanation
Indices: 217337--217395 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
217327 GAAATTAAAT
217337 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
217369 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
217396 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:217692 original size:13 final size:13
Alignment explanation
Indices: 217674--217699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
217664 CAATTTTTTG
217674 TGTATCGATACAT
1 TGTATCGATACAT
217687 TGTATCGATACAT
1 TGTATCGATACAT
217700 ATTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:217710 original size:32 final size:33
Alignment explanation
Indices: 217654--217717 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
217644 TACAAGCCAA
*
217654 TGTATCAATACAATTTTTTGTGTATCGATACAT
1 TGTATCAATACAATATTTTGTGTATCGATACAT
*
217687 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCAATACAATATTTTGTGTATCGATACA
217718 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (33 bp):
TGTATCAATACAATATTTTGTGTATCGATACAT
Found at i:217793 original size:20 final size:20
Alignment explanation
Indices: 217748--217821 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
217738 ATTCCAATGA
***
217748 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
*
217769 CATGTATCGATACATTGCAT
1 CATGTATCGATACATTGAAT
*
217789 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
217809 TGTGTATCGATAC
1 CATGTATCGATAC
217822 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:217822 original size:20 final size:20
Alignment explanation
Indices: 217768--217824 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
217758 TACATCTTTT
* *
217768 TCATGTATCGATACATTGCA
1 TCATGTATCGATACTTTGAA
217788 TCATGTATCGATACTTTGAA
1 TCATGTATCGATACTTTGAA
**
217808 TTGTGTATCGATACTTT
1 TCATGTATCGATACTTT
217825 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TCATGTATCGATACTTTGAA
Found at i:224151 original size:15 final size:14
Alignment explanation
Indices: 224131--224179 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
224121 TAAAATATAA
224131 TAAAAAATATTAAAT
1 TAAAAAA-ATTAAAT
224146 TAAAAAAATTTAAAT
1 TAAAAAAA-TTAAAT
*
224161 TTAAAAAA-TAAAT
1 TAAAAAAATTAAAT
224174 TAAAAA
1 TAAAAA
224180 TATAACTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 10 0.32
14 1 0.03
15 20 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAAAATTAAAT
Found at i:224154 original size:28 final size:28
Alignment explanation
Indices: 224122--224179 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
224112 TTTATATTTT
224122 AAAATAT-AA-TAAAAAATATTAAATTAAA
1 AAAATATAAATTAAAAAA-A-TAAATTAAA
* *
224150 AAAATTTAAATTTAAAAAATAAATTAAA
1 AAAATATAAATTAAAAAAATAAATTAAA
224178 AA
1 AA
224180 TATAACTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 17 0.65
29 3 0.12
30 6 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAATATAAATTAAAAAAATAAATTAAA
Found at i:224166 original size:13 final size:13
Alignment explanation
Indices: 224122--224184 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 13
224112 TTTATATTTT
*
224122 AAAATAT-AATAA
1 AAAATATAAATTA
224134 AAAATATTAAATTAAA
1 AAAATA-TAAATT--A
*
224150 AAAATTTAAATTTA
1 AAAATATAAA-TTA
224164 AAAA-ATAAATTA
1 AAAATATAAATTA
224176 AAAATATAA
1 AAAATATAA
224185 CTTGAACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 13 0.31
13 9 0.21
14 8 0.19
15 4 0.10
16 8 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATAAATTA
Found at i:224265 original size:19 final size:17
Alignment explanation
Indices: 224245--224284 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
224235 AATTTAAATA
224245 AAATAAAATTTATATTTT
1 AAATAAAATTTA-ATTTT
*
224263 AAATTAAATTTAA-TTT
1 AAATAAAATTTAATTTT
224279 AAATAA
1 AAATAA
224285 TTATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATAAAATTTAATTTT
Found at i:224271 original size:18 final size:16
Alignment explanation
Indices: 224235--224284 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
224225 AATATAAACG
* *
224235 AATTTAAATAAAATAA
1 AATTTAATTTAAATAA
*
224251 AATTTATATTTTAAATTA
1 AATTTA-A-TTTAAATAA
224269 AATTTAATTTAAATAA
1 AATTTAATTTAAATAA
224285 TTATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.50
17 2 0.07
18 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAATTTAAATAA
Found at i:224319 original size:43 final size:46
Alignment explanation
Indices: 224242--224328 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 46
224232 ACGAATTTAA
*
224242 ATAAAATAAAATTTATATTTTAAATTAAATTTAATTTAA-ATAATT
1 ATAAAATAAAATTTATATATTAAATTAAATTTAATTTAATATAATT
224287 ATAAAAT-AAA-TTA-ATATTAAACTTAAATTTAATTTAATATAA
1 ATAAAATAAAATTTATATATTAAA-TTAAATTTAATTTAATATAA
224329 ATCTAGTCTC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
42 7 0.18
43 18 0.46
44 7 0.18
45 7 0.18
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (46 bp):
ATAAAATAAAATTTATATATTAAATTAAATTTAATTTAATATAATT
Found at i:224828 original size:16 final size:16
Alignment explanation
Indices: 224807--224870 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
224797 CTAAATTAAT
*
224807 AAATTTGAATTTAAAA
1 AAATTTAAATTTAAAA
224823 AAATTTAAATTTAAAA
1 AAATTTAAATTTAAAA
*
224839 AATTTTAAA-TTAAAA
1 AAATTTAAATTTAAAA
*
224854 AAA-TCAAATTTAAAA
1 AAATTTAAATTTAAAA
224869 AA
1 AA
224871 TTCGAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
14 4 0.09
15 16 0.37
16 23 0.53
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATTTAAATTTAAAA
Found at i:224838 original size:15 final size:15
Alignment explanation
Indices: 224798--224872 Score: 82
Period size: 15 Copynumber: 5.0 Consensus size: 15
224788 TGATTTAATC
*
224798 TAAA-TTAATAAATT
1 TAAATTTAAAAAATT
*
224812 TGAATTTAAAAAAATT
1 TAAATTT-AAAAAATT
224828 TAAATTTAAAAAATTT
1 TAAATTTAAAAAA-TT
*
224844 TAAA-TTAAAAAAAT
1 TAAATTTAAAAAATT
*
224858 CAAATTTAAAAAATT
1 TAAATTTAAAAAATT
224873 CGAAATCAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.14
15 25 0.49
16 19 0.37
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (15 bp):
TAAATTTAAAAAATT
Found at i:224870 original size:31 final size:31
Alignment explanation
Indices: 224802--224878 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
224792 TTAATCTAAA
* * *
224802 TTAATAAATTTGAATTTAAAAAAATTTAAAT
1 TTAAAAAATTTGAAATTAAAAAAATTCAAAT
*
224833 TTAAAAAATTTTAAATTAAAAAAA-TCAAAT
1 TTAAAAAATTTGAAATTAAAAAAATTCAAAT
*
224863 TTAAAAAATTCGAAAT
1 TTAAAAAATTTGAAAT
224879 CAACGTAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (31 bp):
TTAAAAAATTTGAAATTAAAAAAATTCAAAT
Found at i:225088 original size:3 final size:3
Alignment explanation
Indices: 225080--225116 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
225070 GAAAAGATAT
225080 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
225117 ACAATTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:226361 original size:18 final size:18
Alignment explanation
Indices: 226338--226378 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
226328 TTTAGTACAC
226338 AATTTACATT-ATTTTTGA
1 AATTTA-ATTCATTTTTGA
226356 AATTTAATTCCATTTTTGA
1 AATTTAATT-CATTTTTGA
226375 AATT
1 AATT
226379 CAAATTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 6 0.29
19 12 0.57
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (18 bp):
AATTTAATTCATTTTTGA
Found at i:226787 original size:2 final size:2
Alignment explanation
Indices: 226780--226827 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
226770 AAGTAGATAG
226780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
226822 AT AT AT
1 AT AT AT
226828 CGAACTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228964 original size:16 final size:16
Alignment explanation
Indices: 228920--228967 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 16
228910 AATTTGACTT
228920 TTTTTATAAAAATTAA
1 TTTTTATAAAAATTAA
*
228936 TTACTATTAATAATAATTAA
1 TT--T-TT-ATAAAAATTAA
228956 TTTTTATAAAAA
1 TTTTTATAAAAA
228968 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
16 8 0.31
17 2 0.08
18 2 0.08
19 2 0.08
20 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTATAAAAATTAA
Found at i:229193 original size:37 final size:33
Alignment explanation
Indices: 229152--229218 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 33
229142 AAATTTGACT
229152 TTTTATAAAAATTAATTATTATTTAATAGTAATTAAA
1 TTTTATAAAAA--AATTA-TATTT-ATAGTAATTAAA
229189 TTTTATAAAAAAATTATATTTATAGTAATT
1 TTTTATAAAAAAATTATATTTATAGTAATT
229219 TTATAGTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 9 0.30
34 5 0.17
35 5 0.17
37 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTTATAAAAAAATTATATTTATAGTAATTAAA
Found at i:230447 original size:23 final size:23
Alignment explanation
Indices: 230398--230456 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
230388 TTAAAGACTC
230398 AATTGGATTTGA-AATTCGAATT
1 AATTGGATTTGACAATTCGAATT
* *
230420 AATTGGATTTGACCATTCGAGTT
1 AATTGGATTTGACAATTCGAATT
* *
230443 TATTGGGTTTGACA
1 AATTGGATTTGACA
230457 CTCAAGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (23 bp):
AATTGGATTTGACAATTCGAATT
Found at i:230616 original size:28 final size:29
Alignment explanation
Indices: 230570--230631 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
230560 AATTTTATCG
230570 AAATATAACAAATAAATAATATTTAAAAA
1 AAATATAACAAATAAATAATATTTAAAAA
* * *
230599 TAAATATAA-AAAT-GATAATTTTTAATAA
1 -AAATATAACAAATAAATAATATTTAAAAA
230627 AAATA
1 AAATA
230632 AATATCTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 12 0.41
29 4 0.14
30 8 0.28
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
AAATATAACAAATAAATAATATTTAAAAA
Found at i:234094 original size:17 final size:17
Alignment explanation
Indices: 234060--234100 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
234050 GCCTTTGTAA
234060 TTATAAAAATTAAATAT
1 TTATAAAAATTAAATAT
* **
234077 TTGTAAAAATTATTTAT
1 TTATAAAAATTAAATAT
234094 TTATAAA
1 TTATAAA
234101 TTATATAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TTATAAAAATTAAATAT
Found at i:236242 original size:21 final size:22
Alignment explanation
Indices: 236198--236245 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
236188 TTTAATAAAA
236198 AAAATTTATTTAAATTTAATTAT
1 AAAATTTA-TTAAATTTAATTAT
236221 AAAATTTA-TAAATATTAA-TAT
1 AAAATTTATTAAAT-TTAATTAT
236242 AAAA
1 AAAA
236246 ATAATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.50
22 4 0.17
23 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTTATTAAATTTAATTAT
Found at i:236246 original size:22 final size:21
Alignment explanation
Indices: 236197--236247 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
236187 ATTTAATAAA
236197 AAAAATTTATTTAAATTTAATT
1 AAAAATTTA-TTAAATTTAATT
236219 ATAAAATTTA-TAAATATTAATAT
1 A-AAAATTTATTAAAT-TTAAT-T
236242 AAAAAT
1 AAAAAT
236248 AATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.19
22 11 0.42
23 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAATTTATTAAATTTAATT
Found at i:237404 original size:27 final size:28
Alignment explanation
Indices: 237366--237420 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
237356 AATGAGATAG
*
237366 AAAAATATAATTGTATAACT-ATTTTTA
1 AAAAATATAATTGTAAAACTCATTTTTA
*
237393 AAAAACTA-AATTTTAAAACTCATTTTTA
1 AAAAA-TATAATTGTAAAACTCATTTTTA
237421 TCTATCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (28 bp):
AAAAATATAATTGTAAAACTCATTTTTA
Found at i:243248 original size:2 final size:2
Alignment explanation
Indices: 243241--243277 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
243231 AAAATTATCT
243241 TA TA TA TA TGA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
243278 TTTTTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:243250 original size:20 final size:22
Alignment explanation
Indices: 243218--243271 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
243208 ATACATTTCA
*
243218 ATATATATGTATGAAAAT-TAT
1 ATATATATATATGAAAATATAT
* *
243239 CT-TATATATATGAATATATAT
1 ATATATATATATGAAAATATAT
243260 ATATATATATAT
1 ATATATATATAT
243272 ATATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 13 0.48
21 5 0.19
22 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATATATATATGAAAATATAT
Found at i:243399 original size:11 final size:11
Alignment explanation
Indices: 243380--243426 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
243370 CTCTAACTTG
243380 TTTTATTTTTA
1 TTTTATTTTTA
*
243391 TTTTCTTTTTA
1 TTTTATTTTTA
*
243402 TTTTAGTTTTA
1 TTTTATTTTTA
243413 TCTTT-TTCTTTA
1 T-TTTATT-TTTA
243425 TT
1 TT
243427 CATCAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:243799 original size:6 final size:6
Alignment explanation
Indices: 243782--243817 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
243772 TTAATAAAAA
* *
243782 TTATTT TTATAT TAATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
243818 ATTTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:244270 original size:16 final size:16
Alignment explanation
Indices: 244230--244271 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
244220 CACAAAAAAA
*
244230 TTAA-CTAAATGATAT
1 TTAAGCTAAATGATAG
*
244245 TTAAGTTAAATGATAG
1 TTAAGCTAAATGATAG
*
244261 TTATGCTAAAT
1 TTAAGCTAAAT
244272 TTAAACCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (16 bp):
TTAAGCTAAATGATAG
Found at i:244946 original size:2 final size:2
Alignment explanation
Indices: 244939--244982 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
244929 AATAGAGTAA
244939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244981 AT
1 AT
244983 CTGATGAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245185 original size:2 final size:2
Alignment explanation
Indices: 245178--245211 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
245168 ATTAACATCA
245178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245212 CTTGATTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247171 original size:7 final size:7
Alignment explanation
Indices: 247161--247219 Score: 57
Period size: 7 Copynumber: 7.7 Consensus size: 7
247151 AAAAAGAGAA
247161 AAAAATT
1 AAAAATT
247168 AAAAA-T
1 AAAAATT
247174 ATAAAATT
1 A-AAAATT
247182 AAAAATT
1 AAAAATT
247189 AAAAATAAT
1 AAAAAT--T
247198 ATAAAATTT
1 A-AAAA-TT
247207 AAACAATT
1 AAA-AATT
247215 AAAAA
1 AAAAA
247220 AATCCAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
6 2 0.04
7 23 0.51
8 9 0.20
9 6 0.13
10 4 0.09
11 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:247186 original size:24 final size:23
Alignment explanation
Indices: 247159--247219 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
247149 GAAAAAAGAG
247159 AAAAAAATTAAAAATATAAAATT
1 AAAAAAATTAAAAATATAAAATT
247182 --AAAAATTAAAAATAATATAAAATT
1 AAAAAAATT--AAA-AATATAAAATT
* *
247206 TAAACAATTAAAAA
1 AAAAAAATTAAAAA
247220 AATCCAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
21 7 0.22
23 5 0.16
24 14 0.44
26 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAAAATTAAAAATATAAAATT
Found at i:247229 original size:25 final size:22
Alignment explanation
Indices: 247161--247222 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 22
247151 AAAAAGAGAA
*
247161 AAAAATTAAAAATATAAAA-TT
1 AAAAATTAAAAAAATAAAATTT
247182 AAAAATTAAAAATAATATAAAATTT
1 AAAAATT-AAAA-AA-ATAAAATTT
247207 AAACAATTAAAAAAAT
1 AAA-AATTAAAAAAAT
247223 CCAAAATCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 7 0.20
22 4 0.11
23 3 0.09
24 8 0.23
25 9 0.26
26 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATTAAAAAAATAAAATTT
Found at i:247239 original size:25 final size:26
Alignment explanation
Indices: 247160--247240 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 26
247150 AAAAAAGAGA
247160 AAAAAATTAAAAAT-AT--AAAAT--
1 AAAAAATTAAAAATAATACAAAATCC
* * **
247181 TAAAAATTAAAAATAATATAAAATTT
1 AAAAAATTAAAAATAATACAAAATCC
* *
247207 AAACAATTAAAAA-AATCCAAAATCC
1 AAAAAATTAAAAATAATACAAAATCC
247232 AAAAAATTA
1 AAAAAATTA
247241 TAATTTAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 13 0.28
22 2 0.04
24 5 0.11
25 16 0.34
26 11 0.23
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAAATTAAAAATAATACAAAATCC
Found at i:247390 original size:35 final size:37
Alignment explanation
Indices: 247325--247412 Score: 103
Period size: 36 Copynumber: 2.4 Consensus size: 37
247315 AATATATTGA
* *
247325 AAAAATAATTAAAAATATAAAAATAGTTTTT-AAATTC
1 AAAAAT-ATAAAAAATATAAAAACAGTTTTTGAAATTC
*
247362 AAAAATATAAAAAAT-TGAAAAACA-TTTTTGAAATTT
1 AAAAATATAAAAAATAT-AAAAACAGTTTTTGAAATTC
247398 AAAAA-ATAAAAAATA
1 AAAAATATAAAAAATA
247413 AACATTCAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
35 15 0.33
36 24 0.53
37 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (37 bp):
AAAAATATAAAAAATATAAAAACAGTTTTTGAAATTC
Found at i:248120 original size:18 final size:18
Alignment explanation
Indices: 248099--248143 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
248089 TTAATTTTTA
248099 TATATTTTTTGTATTGTT
1 TATATTTTTTGTATTGTT
* *
248117 TATA-TTTTTCTATTTTT
1 TATATTTTTTGTATTGTT
248134 TA-ATTTTTTG
1 TATATTTTTTG
248144 AATTTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 18 0.78
18 4 0.17
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (18 bp):
TATATTTTTTGTATTGTT
Found at i:248148 original size:17 final size:18
Alignment explanation
Indices: 248078--248148 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
248068 AAAATTTTTG
* *
248078 TTTTCTATTTATT-AATT
1 TTTTATATTTTTTGAATT
*
248095 TTTATATATTTTTTGTATT
1 TTT-TATATTTTTTGAATT
*
248114 GTTTATATTTTTCT--ATT
1 TTTTATATTTTT-TGAATT
248131 TTTTA-ATTTTTTGAATT
1 TTTTATATTTTTTGAATT
248148 T
1 T
248149 AAATAATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.02
16 6 0.14
17 14 0.32
18 17 0.39
19 6 0.14
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTATATTTTTTGAATT
Found at i:248298 original size:16 final size:18
Alignment explanation
Indices: 248277--248314 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
248267 TTTTATAATA
248277 TTTTGAA-T-TTTTATTT
1 TTTTGAATTGTTTTATTT
248293 TTTTGAATTGTTTTATTT
1 TTTTGAATTGTTTTATTT
248311 TTTT
1 TTTT
248315 TCTAGTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTTGAATTGTTTTATTT
Found at i:248433 original size:19 final size:18
Alignment explanation
Indices: 248404--248462 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
248394 TGATAGATAC
*
248404 TTTTA-ATTTTTTTGAAT
1 TTTTATATTTTTTTAAAT
*
248421 TATTTATATTTTTTAAAAT
1 T-TTTATATTTTTTTAAAT
*
248440 TTTTATAATTTTTCTAAAT
1 TTTTAT-ATTTTTTTAAAT
248459 TTTT
1 TTTT
248463 TCTAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 9 0.26
19 25 0.71
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATATTTTTTTAAAT
Found at i:248478 original size:19 final size:19
Alignment explanation
Indices: 248411--248479 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
248401 TACTTTTAAT
* *
248411 TTTTTTGAATTATTTAT-A
1 TTTTTTAAATTTTTTATAA
*
248429 TTTTTTAAAATTTTTATAA
1 TTTTTTAAATTTTTTATAA
*
248448 TTTTTCTAAATTTTTTCTAA
1 TTTTT-TAAATTTTTTATAA
*
248468 TTTTTTGAATTT
1 TTTTTTAAATTT
248480 AAAAAGACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 14 0.33
19 12 0.28
20 17 0.40
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTAAATTTTTTATAA
Found at i:253113 original size:52 final size:52
Alignment explanation
Indices: 252964--253092 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
252954 CGAAATATGA
252964 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
253016 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
253068 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
253093 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:253199 original size:13 final size:13
Alignment explanation
Indices: 253174--253263 Score: 54
Period size: 13 Copynumber: 5.9 Consensus size: 13
253164 ACAAAACTTA
253174 TGTATCTGATACAT
1 TGTATC-GATACAT
253188 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
253206 ATGTATCGATACAT
1 -TGTATCGATACAT
253220 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
253238 ATTTATCGATACAT
1 -TGTATCGATACAT
253252 TGTATCGATACA
1 TGTATCGATACA
253264 ACACTTTATG
Statistics
Matches: 62, Mismatches: 2, Indels: 25
0.70 0.02 0.28
Matches are distributed among these distances:
13 23 0.37
14 8 0.13
16 12 0.19
18 2 0.03
19 17 0.27
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:253222 original size:32 final size:32
Alignment explanation
Indices: 253153--253281 Score: 222
Period size: 32 Copynumber: 4.0 Consensus size: 32
253143 AGTAGCTTAT
*
253153 ATTGTATCGATACAAAACTTATGTATCTGATAC
1 ATTGTATCGATACAACACTTATGTATC-GATAC
253186 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
253218 ATTGTATCGATACAACACTTATTTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
253250 ATTGTATCGATACAACACTTTATGTATCGATA
1 ATTGTATCGATACAACAC-TTATGTATCGATA
253282 TAAATCGTTG
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 54 0.59
33 38 0.41
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:253229 original size:65 final size:65
Alignment explanation
Indices: 253153--253281 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
253143 AGTAGCTTAT
253153 ATTGTATCGATACAAAACTTATGTATCTGATACATTGTATCGATACAACAC-TTATGTATCGATA
1 ATTGTATCGATACAAAACTTATGTATC-GATACATTGTATCGATACAACACTTTATGTATCGATA
253217 C
65 C
* *
253218 ATTGTATCGATACAACACTTATTTATCGATACATTGTATCGATACAACACTTTATGTATCGATA
1 ATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGATA
253282 TAAATCGTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 23 0.38
65 38 0.62
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (65 bp):
ATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:254126 original size:20 final size:20
Alignment explanation
Indices: 254101--254155 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
254091 TTTTCACAAT
* *
254101 TTGTATCGATGCATTGTTCA
1 TTGTATCGATACATTATTCA
254121 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
*
254141 TTGTATCAATACATT
1 TTGTATCGATACATT
254156 CTGGGTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:256648 original size:79 final size:78
Alignment explanation
Indices: 256504--256725 Score: 275
Period size: 79 Copynumber: 2.8 Consensus size: 78
256494 TCTTCATCTC
* * * *
256504 GGGGATACTCCAACCTCGGTTTTATGTTC-AAAACATCAATTTTTCATAATCGGGGATACTTCAA
1 GGGGATACTCCAACC-CGATTTTAT-TTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAA
*
256568 TCCTGTTATTTTCGA
64 TCCTGTCATTTTCGA
* * * * *
256583 GGGGATACTCCAATCCCGATTTTATTCCTAAAACACCAGTTTTTCACAATTGAGGATTCTCCAAT
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAT
*
256648 CTTGTCATTTTCGA
65 CCTGTCATTTTCGA
* * *
256662 GGTGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAA
256726 CTTTGATTTT
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 2 0.02
79 117 0.97
80 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAATC
CTGTCATTTTCGA
Found at i:256725 original size:51 final size:51
Alignment explanation
Indices: 256665--256832 Score: 246
Period size: 51 Copynumber: 3.3 Consensus size: 51
256655 TTTTCGAGGT
* *
256665 GATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGG
***
256716 GATACTCCAACTTTGATTTTATTTCCAAAACACCAATTTTCCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGG
* * * *
256767 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAATCGAG
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGG
*
256818 GATACTCTAACCCCG
1 GATACTCCAACCCCG
256833 TTATTTCATC
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 105 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGG
Found at i:256936 original size:51 final size:51
Alignment explanation
Indices: 256871--256988 Score: 182
Period size: 51 Copynumber: 2.3 Consensus size: 51
256861 CTATTTTCGA
* * *
256871 GGGGATACTCCAACCCTGGCTTTATTTTTAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCTAGCCTTATTTCTAAAATATTGATTTCTCACAATC
* * *
256922 GGGGATACTTCAACCCTAGCCTTATTTCTAAATTATTGATTTTTCACAATC
1 GGGGATACTCCAACCCTAGCCTTATTTCTAAAATATTGATTTCTCACAATC
256973 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
256989 CGTTATTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (51 bp):
GGGGATACTCCAACCCTAGCCTTATTTCTAAAATATTGATTTCTCACAATC
Found at i:257057 original size:79 final size:80
Alignment explanation
Indices: 256959--257151 Score: 268
Period size: 79 Copynumber: 2.4 Consensus size: 80
256949 CTAAATTATT
* *
256959 GATTTTTCACAATC-GGGGATACTCCAACCCCGTTATTT-TCGAG-GACATACTCCAACCCCGAT
1 GATTTTCCATAATCAGGGGATACTCCAACCCCGTTATTTCT-GAGAGA-ATACTCCAACCCCGAT
*
257021 TTTATTTTCAAAATACC
64 TTTATTTTCAAAACACC
* * *
257038 GATTTTCTATAATTA-GGGATACTCCAACCCTGTTATTTCTGAGAGAATACTCCAACCCCGATTT
1 GATTTTCCATAATCAGGGGATACTCCAACCCCGTTATTTCTGAGAGAATACTCCAACCCCGATTT
*
257102 TATTTTCAAAACACT
66 TATTTTCAAAACACC
*
257117 GATTTTCCATAATCAGGGGATACTCCAGCCCCGTT
1 GATTTTCCATAATCAGGGGATACTCCAACCCCGTT
257152 GTTATCTCCA
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
79 79 0.80
80 20 0.20
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (80 bp):
GATTTTCCATAATCAGGGGATACTCCAACCCCGTTATTTCTGAGAGAATACTCCAACCCCGATTT
TATTTTCAAAACACC
Found at i:258674 original size:20 final size:19
Alignment explanation
Indices: 258646--258719 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 19
258636 AATTGTAAAA
*
258646 ATAACATTTTAATAATAATT
1 ATAATATTTTAATAATAA-T
* *
258666 ATAATATTTTAAATATTTAT
1 ATAATATTTT-AATAATAAT
*
258686 ATAATTATTTTAATAGTAAAT
1 ATAA-TATTTTAATAAT-AAT
*
258707 AGTATTATTTTAA
1 A-TAATATTTTAA
258720 GTATTTAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 19 0.43
21 23 0.52
22 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (19 bp):
ATAATATTTTAATAATAAT
Found at i:258770 original size:14 final size:14
Alignment explanation
Indices: 258747--258801 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
258737 AATATTTTAG
258747 CATT-AAATATTAT
1 CATTAAAATATTAT
258760 CATTAAAATATTA-
1 CATTAAAATATTAT
258773 CAATTTAAAATATTAAT
1 C-A-TTAAAATATT-AT
258790 -ATTAAAA-ATTAT
1 CATTAAAATATTAT
258802 TAGTTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.05
13 8 0.22
14 15 0.41
15 11 0.30
16 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
CATTAAAATATTAT
Found at i:258837 original size:22 final size:22
Alignment explanation
Indices: 258812--258853 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
258802 TAGTTTAATT
*
258812 ATAAATAATTTTTAATATTTTA
1 ATAAATAATATTTAATATTTTA
*
258834 ATAATTAATATTTAATATTT
1 ATAAATAATATTTAATATTT
258854 ATGTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAAATAATATTTAATATTTTA
Found at i:261173 original size:20 final size:21
Alignment explanation
Indices: 261148--261201 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
261138 GTTACAAGCT
*
261148 ATGTATCAATACAATT-CATC
1 ATGTATCGATACAATTGCATC
*
261168 ATGTATCGATAC-ATTGTATC
1 ATGTATCGATACAATTGCATC
261188 ATGTATCGATACAA
1 ATGTATCGATACAA
261202 ACAGTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTGCATC
Found at i:261274 original size:19 final size:20
Alignment explanation
Indices: 261230--261284 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
261220 CTGCCAATCT
**
261230 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
261250 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
261269 CATGTATCGATACAAT
1 CATGTATCGATACAAT
261285 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:261288 original size:13 final size:13
Alignment explanation
Indices: 261270--261296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
261260 TACAATTAAC
261270 ATGTATCGATACA
1 ATGTATCGATACA
261283 ATGTATCGATACA
1 ATGTATCGATACA
261296 A
1 A
261297 GGCATAATGT
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:263823 original size:13 final size:13
Alignment explanation
Indices: 263803--263876 Score: 70
Period size: 13 Copynumber: 6.2 Consensus size: 13
263793 AATAGTACTT
*
263803 AATGTATCGATAT
1 AATGTATCGATAC
*
263816 AGTGTATCGATAC
1 AATGTATCGATAC
263829 AATGTATCGATAC
1 AATGTATCGATAC
*
263842 AA-G----GA-AT
1 AATGTATCGATAC
*
263849 ATTGTATCGATAC
1 AATGTATCGATAC
263862 AATGTATCGATAC
1 AATGTATCGATAC
263875 AA
1 AA
263877 GGAATATTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
12 3 0.06
13 40 0.83
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:263856 original size:20 final size:20
Alignment explanation
Indices: 263831--263895 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
263821 ATCGATACAA
263831 TGTATCGATACAAGGAATAT
1 TGTATCGATACAAGGAATAT
263851 TGTATCGATAC-----A-A-
1 TGTATCGATACAAGGAATAT
263864 TGTATCGATACAAGGAATAT
1 TGTATCGATACAAGGAATAT
263884 TGTATCGATACA
1 TGTATCGATACA
263896 TCTGGGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAGGAATAT
Found at i:263860 original size:33 final size:33
Alignment explanation
Indices: 263818--263895 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
263808 ATCGATATAG
263818 TGTATCGATACAATGTATCGATACAAGGAATAT
1 TGTATCGATACAATGTATCGATACAAGGAATAT
263851 TGTATCGATACAATGTATCGATACAAGGAATAT
1 TGTATCGATACAATGTATCGATACAAGGAATAT
263884 TGTATCGATACA
1 TGTATCGATACA
263896 TCTGGGTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACAAGGAATAT
Found at i:269259 original size:28 final size:28
Alignment explanation
Indices: 269223--269281 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
269213 GAATCCGTTG
269223 AAGGAGGTTAGGCTCTAATACCAATTGA
1 AAGGAGGTTAGGCTCTAATACCAATTGA
269251 AAGGAGGTTAGGCTCTAATACCAATTGA
1 AAGGAGGTTAGGCTCTAATACCAATTGA
269279 AAG
1 AAG
269282 CTCAAGGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (28 bp):
AAGGAGGTTAGGCTCTAATACCAATTGA
Found at i:270102 original size:13 final size:13
Alignment explanation
Indices: 270084--270108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
270074 CAATTATCCA
270084 TGTATCGATACAT
1 TGTATCGATACAT
270097 TGTATCGATACA
1 TGTATCGATACA
270109 AAGCATAATA
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:274124 original size:16 final size:16
Alignment explanation
Indices: 274103--274161 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
274093 TACATAATTT
274103 TATTTAATATTTATTA
1 TATTTAATATTTATTA
*
274119 TATTTAATACTTATT-
1 TATTTAATATTTATTA
274134 TATTATTAA-ATTTA-TA
1 TA-T-TTAATATTTATTA
274150 TATTTAATATTT
1 TATTTAATATTT
274162 CAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 4 0.11
15 8 0.22
16 21 0.57
17 4 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTAATATTTATTA
Found at i:274171 original size:31 final size:32
Alignment explanation
Indices: 274091--274171 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 32
274081 TCATTTAGTC
*
274091 AATACATAATTTTATTTAATATTTATTATATTT
1 AATACTTAATTTTA-TTAATATTTATTATATTT
*
274124 AATACTTATTTATTATTAA-ATTTA-TATATTT
1 AATACTTAATT-TTATTAATATTTATTATATTT
*
274155 AATATTTCAATTTTATT
1 AATACTT-AATTTTATT
274172 TTACTACAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 18 0.43
32 8 0.19
33 13 0.31
34 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (32 bp):
AATACTTAATTTTATTAATATTTATTATATTT
Found at i:274308 original size:2 final size:2
Alignment explanation
Indices: 274301--274330 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
274291 TCTGTTTTAC
274301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
274331 CAAGTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276734 original size:670 final size:663
Alignment explanation
Indices: 275357--277294 Score: 2412
Period size: 669 Copynumber: 2.9 Consensus size: 663
275347 AAAGCTAATA
* *
275357 TAACTAGCCTAACATTAGGTAATTACAATTTTCTTATTAATAATTTTAATTATTACTATTTTCTT
1 TAACTAGCCTAAAATTAGGTAATTACAATTTTCTTATTAATAATTTTAATTATTACTATTTTTTT
* * * *
275422 ATATATAAATAGTTTTTATAATTA-TAATAAATGTAAAAA----GATTCCGTAACGCTTATATCT
66 ATATATAAATAGTTTTTATTATTACT-GTAAATGTAAAAATTTTGAGTCCG-AACGCTTAGATCT
* * * *
275482 AATTTTCATTTTTTTTTTTGCCTTAAAACTTTAAAAGACTTTGAAAGATCTTTTCTATAAATAAC
129 AATTTTCACTTTTTTTTGTGCCTTAAAACTTTAAAAGACTTTAAAAGATTTTTTCTATAAAT-AC
* * * * * *
275547 TTTACTAA---TTTCGTCCTGTTTACAATAATCTTTTTAAAAGTATTCTTAATATTACTTTTTCA
193 -TCAC-AACTCTTTCGTCATGTTTACAATAATCTTTTCAAAGGTATTCTAAATATTGCTTTTTCA
* * * *
275609 ACTTTTCACTCAATTCTTAAGTTTTCAAAAGAATTTAACACAATTTTCAATATTATAATTCTAAT
256 AC-TTTCACTCTATTCTTAAGTTTTCAAAAGAATCTAACACCATTTTC-ATATTTTAATTCTAAT
* ** *
275674 ATATACGAAATTAGTTTTTTAGTAAAAGCTTGTATAAAAAATGTGCGAAAAAAAT-TTTAAAATA
319 ATATGCGAAATTAGTTTTTTAGTAAAAGC-T-TA-AAAAAATGCAC-AAAAAAATGTTTGAAATA
* *
275738 ATAA-TTTTTT-ATATGTTGTATGCTTTTATTTAAATTTTATAAATGCAAAACTTATTTAAAAAT
380 ATAATTTTTTTGTTATGTTGAATGCTTTTATTTAAATTTTATAAATGCAAAACTTATTTAAAAAT
*
275801 CATATTAAATCTAATTAATAAACATTGTTTTGTTTATTAATATAAATAATTTTATTAATTTTGAT
445 CATATTAAATTTAATTAATAAACATTGTTTTGTTTATTAATATAAATAATTTTATTAATTTTGAT
* * * *
275866 T-TCTATATAAGAATTTTTTGTAAAAAAATCAATCATAATATCTATTGTTTCTAACATTTGTTTA
510 TCT-TATATAAGAA-TTTTTGTAAAAAAATCAATTATAATATCTATTGTTTTTAACATTTATCTA
* * * * *
275930 CAATTATAATTAGAAAATTTTTTAGCCACGTTCTATATAGATAGAATTTTAATTTTGATTTATAT
573 CAATTTTAATTACAAAATTTTTTAGCCACGTTTTACATAGATAGAATTTTAATTTTAATTTATAT
275995 ATAAGAATTTCTTATCTAGGCTAACC
638 ATAAGAATTTCTTATCTAGGCTAACC
*
276021 TAACTAGCCTAAAATTAGGTAATTACAATTTACTTATTAATAATTTTAATTATTACTACTTTTTT
1 TAACTAGCCTAAAATTAGGTAATTACAATTTTCTTATTAATAATTTTAATTATTACTA-TTTTTT
* *
276086 TATATATATATAGTTTTTATTATTACTGTAAATGTAAAAATTTTGAGTCCGAAACGCTTAGATTT
65 TATATATAAATAGTTTTTATTATTACTGTAAATGTAAAAATTTTGAGTCCG-AACGCTTAGATCT
** * * * *
276151 AATTTTCACTTTTTTTTGTGCCTTCGAACCTCAAAATACTTTATAAAGATTTTTTCTATAAGTAC
129 AATTTTCACTTTTTTTTGTGCCTTAAAACTTTAAAAGACTTTA-AAAGATTTTTTCTATAAATAC
** * *
276216 TCACAACTCTTTTATCATGTTTACAATAATCTTTTCAAAGGTATTCTCAATATTGCTTCTTCAAC
193 TCACAACTCTTTCGTCATGTTTACAATAATCTTTTCAAAGGTATTCTAAATATTGCTTTTTCAAC
* * *
276281 TTTCACTCTATTCTTAAGTTTT-ACAAAGAATCGAATACCATTTTCTATGTTTTAATTCTAATAT
258 TTTCACTCTATTCTTAAGTTTTCA-AAAGAATCTAACACCATTTTC-ATATTTTAATTCTAATAT
**
276345 ATGCGAAATTAGTTTTTTAAAAAAAGCTTCCACAAAAAATGCACAAAAAAATGTTTGAAATAATA
321 ATGCGAAATTAGTTTTTTAGTAAAAGCTT--A-AAAAAATGCACAAAAAAATGTTTGAAATAATA
* * *
276410 ATTTTTTTTGTTATATTGCATGCTTTTATTTAAATTTTATAAATGCAAAACCTATTTAAAAATCA
383 A-TTTTTTTGTTATGTTGAATGCTTTTATTTAAATTTTATAAATGCAAAACTTATTTAAAAATCA
*
276475 TATTAAATTTAATTAATAAACATTATTTTGTTTATTAATATAAAT-ATTTTATTAATTTTGATTC
447 TATTAAATTTAATTAATAAACATTGTTTTGTTTATTAATATAAATAATTTTATTAATTTTGATTC
*
276539 TTATATAAGAATTTCTTGTAAAAAAATCAATTATAATATCTATTGTTTTTGACATTTATCTACAA
512 TTATATAAGAATTT-TTGTAAAAAAATCAATTATAATATCTATTGTTTTTAACATTTATCTACAA
* * **
276604 TTTTATTTACAAGATTTTTTAGCCA-GCTTTTACATAG-TTTAATTTTAATTTTAATTCT-TATA
576 TTTTAATTACAAAATTTTTTAGCCACG-TTTTACATAGATAGAATTTTAATTTTAATT-TATATA
*
276666 TAAGAATTTCTTATCTATGCTAACC
639 TAAGAATTTCTTATCTAGGCTAACC
* * * *
276691 TAACTAGCTTAATATTAGGTAATTGCAATTTTTTTATTAATAATTTTAATTATTACTATTTTTAT
1 TAACTAGCCTAAAATTAGGTAATTACAATTTTCTTATTAATAATTTTAATTATTACTATTTTT-T
* * ** *
276756 TATATATAGATAGTTTTCATTATTACTGTAAATGTAAAAATTTTGAGTTTGAAGGCTTAGATCTA
65 TATATATAAATAGTTTTTATTATTACTGTAAATGTAAAAATTTTGAGTCCGAACGCTTAGATCTA
* * **
276821 ATTTTCACTTTTTTTTTTGTGCTTTTAAGTTTTAAAAGACTTTGAAAAGATGTTTTT-TATAAAT
130 ATTTTCAC--TTTTTTTTGTGCCTTAAAACTTTAAAAGACTTT-AAAAGAT-TTTTTCTATAAAT
* * * * * *
276885 ACCCACACCTCTCTCGTTATTTTTACAAT-A--TTTTCAAAGGCATTCTAAATATTGCTTTTTCA
191 ACTCACAACTCTTTCGTCATGTTTACAATAATCTTTTCAAAGGTATTCTAAATATTGCTTTTTCA
* *
276947 ATTTTTCACT-TAATTCTTAAGTTTTCAAAAGAATCTAACATCATTTTACATATTTTAATTCTAA
256 A-CTTTCACTCT-ATTCTTAAGTTTTCAAAAGAATCTAACACCATTTT-CATATTTTAATTCTAA
** * * *
277011 TATATGTAAAATTGGTTTTTTAGTAAAAGC-T-------TGCACGAAAAAATGTTTGAAATATTA
318 TATATGCGAAATTAGTTTTTTAGTAAAAGCTTAAAAAAATGCACAAAAAAATGTTTGAAATAATA
* * ** *
277068 ATTTTTTTGTTATGTTAAATGTTTTTATTTAAATTTTATAAATATAAAA-TTATTTAAAAATAAT
383 ATTTTTTTGTTATGTTGAATGCTTTTATTTAAATTTTATAAATGCAAAACTTATTTAAAAATCAT
*
277132 ATCAAATTTAATTAATAAACATTGTTTTGTTTATTAATATAACATAATTTTATTAATTTTGATTC
448 ATTAAATTTAATTAATAAACATTGTTTTGTTTATTAATATAA-ATAATTTTATTAATTTTGATTC
* * * *
277197 TTATATAAGAATTTTT-TAAAAAAAATCAATTATACTATTTATT-TTTTTTACATTTATCTAAAA
512 TTATATAAGAATTTTTGT-AAAAAAATCAATTATAATATCTATTGTTTTTAACATTTATCTACAA
* *
277260 TTTTAATTATAATATTTTTTAGCCACGTTTTACAT
576 TTTTAATTACAAAATTTTTTAGCCACGTTTTACAT
277295 CTATATAATA
Statistics
Matches: 1116, Mismatches: 124, Indels: 76
0.85 0.09 0.06
Matches are distributed among these distances:
656 102 0.09
657 70 0.06
658 58 0.05
664 56 0.05
665 40 0.04
666 1 0.00
667 3 0.00
668 45 0.04
669 255 0.23
670 217 0.19
671 168 0.15
672 101 0.09
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (663 bp):
TAACTAGCCTAAAATTAGGTAATTACAATTTTCTTATTAATAATTTTAATTATTACTATTTTTTT
ATATATAAATAGTTTTTATTATTACTGTAAATGTAAAAATTTTGAGTCCGAACGCTTAGATCTAA
TTTTCACTTTTTTTTGTGCCTTAAAACTTTAAAAGACTTTAAAAGATTTTTTCTATAAATACTCA
CAACTCTTTCGTCATGTTTACAATAATCTTTTCAAAGGTATTCTAAATATTGCTTTTTCAACTTT
CACTCTATTCTTAAGTTTTCAAAAGAATCTAACACCATTTTCATATTTTAATTCTAATATATGCG
AAATTAGTTTTTTAGTAAAAGCTTAAAAAAATGCACAAAAAAATGTTTGAAATAATAATTTTTTT
GTTATGTTGAATGCTTTTATTTAAATTTTATAAATGCAAAACTTATTTAAAAATCATATTAAATT
TAATTAATAAACATTGTTTTGTTTATTAATATAAATAATTTTATTAATTTTGATTCTTATATAAG
AATTTTTGTAAAAAAATCAATTATAATATCTATTGTTTTTAACATTTATCTACAATTTTAATTAC
AAAATTTTTTAGCCACGTTTTACATAGATAGAATTTTAATTTTAATTTATATATAAGAATTTCTT
ATCTAGGCTAACC
Found at i:278450 original size:6 final size:6
Alignment explanation
Indices: 278439--278481 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
278429 TAATTCAATA
* *
278439 AATTAT AATTAT AATTAT AATTAT AATTTT TATTAT -ATTAT AA
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AA
278482 AAAAATTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AATTAT
Found at i:278562 original size:17 final size:17
Alignment explanation
Indices: 278516--278564 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
278506 TATACAATTG
*
278516 AAATAAATATGTTTATA
1 AAATAAATATATTTATA
* *
278533 TAATATTATATATTTATA
1 AAATA-AATATATTTATA
278551 AAATAAATATATTT
1 AAATAAATATATTT
278565 TATATTTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
AAATAAATATATTTATA
Found at i:278896 original size:16 final size:16
Alignment explanation
Indices: 278875--278908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
278865 ACCTAAAAAA
278875 CTTAATAATAAATAAT
1 CTTAATAATAAATAAT
**
278891 CTTAATTTTAAATAAT
1 CTTAATAATAAATAAT
278907 CT
1 CT
278909 AGTAATATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
CTTAATAATAAATAAT
Found at i:279773 original size:18 final size:17
Alignment explanation
Indices: 279736--279778 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
279726 GGAAAAAAAC
279736 TTATGAAAATGAATGAA
1 TTATGAAAATGAATGAA
*
279753 TTATTGAAAACTGAAT-TA
1 TTA-TGAAAA-TGAATGAA
279771 TTATGAAA
1 TTATGAAA
279779 TAAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (17 bp):
TTATGAAAATGAATGAA
Found at i:282879 original size:2 final size:2
Alignment explanation
Indices: 282874--282912 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
282864 TGTGTACATT
282874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
282913 GTGAGGTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:289949 original size:33 final size:33
Alignment explanation
Indices: 289886--289951 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
289876 CTGTATCATG
289886 TATACCATGATATACCAATATTTCATATCCATAA
1 TATACCATGATATA-CAATATTTCATATCCATAA
289920 TATACCATGGATATGA-AATA-TTCATATCCATA
1 TATACCAT-GATAT-ACAATATTTCATATCCATA
289952 TTTCATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 12 0.40
34 12 0.40
35 5 0.17
36 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (33 bp):
TATACCATGATATACAATATTTCATATCCATAA
Found at i:290760 original size:32 final size:33
Alignment explanation
Indices: 290692--290764 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
290682 TGACTGTATC
*
290692 CATAT-CATGCATACCATGCTATATCAATATTA
1 CATATCCATGCATACCATGCGATATCAATATTA
*
290724 CATATCCATGCTATACCATG-GATATTAATATT-
1 CATATCCATGC-ATACCATGCGATATCAATATTA
290756 CATATCCAT
1 CATATCCAT
290765 ATTTCATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 14 0.38
33 15 0.41
34 8 0.22
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (33 bp):
CATATCCATGCATACCATGCGATATCAATATTA
Found at i:293417 original size:12 final size:12
Alignment explanation
Indices: 293400--293424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
293390 AACATTCAGT
293400 AATCTTTGACTA
1 AATCTTTGACTA
293412 AATCTTTGACTA
1 AATCTTTGACTA
293424 A
1 A
293425 TAGATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AATCTTTGACTA
Found at i:295848 original size:11 final size:11
Alignment explanation
Indices: 295832--295869 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
295822 TGATGAGGAT
295832 TATTTTAAAAA
1 TATTTTAAAAA
295843 TATTTTAAAAA
1 TATTTTAAAAA
**
295854 T-TCCTAAAAA
1 TATTTTAAAAA
295864 TATTTT
1 TATTTT
295870 TCTTAGTGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:297742 original size:20 final size:20
Alignment explanation
Indices: 297717--297754 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
297707 GTAAAAACAT
297717 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
297737 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
297755 TGGGTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:298393 original size:29 final size:29
Alignment explanation
Indices: 298322--299344 Score: 1236
Period size: 28 Copynumber: 35.4 Consensus size: 29
298312 CACTAATTTG
* *
298322 TGTGGGCTTTGAAAAAAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
* *
298352 CGTATGGGTTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298383 TGTGGGCTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
298411 TGTGGGCTTTAAAAAGAGTACCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298440 TGTGGGCTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298468 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298496 TATGGGCTTTGAAAGGA-TGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298524 TATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298553 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
298581 TGTGGGCTTTAAAAAGAGTGCCACTAATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298610 TGTGGGCTTTG-AAAGGGTGCCAATGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298638 TGCATGGGCTCTGAAAA-AGTGCCACTGACT
1 TG--TGGGCTTTGAAAAGAGTGCCACTGACT
* *
298668 TGTGGGCTTTGAAAGGA-TGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
298696 TGTGGGTTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298724 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298753 TGTGGGCTTTGAAGAGAGTGCCACCGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* **
298782 TGTGGGCTTTGAAAAAAGTTGCCACCAACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
298812 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298843 TGTGGGCTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298871 TATGGGCTTTGAAAAGAGTACCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
298900 TATGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298928 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
298957 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
*
298987 CGTGTGGGCTTTGAAAAGAGTGCGACTGACT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
299018 TGTGGGCTTTG-AAAGGGTGCCACTGAAT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
299046 TATGGGCTTTGAAAAG-GTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
299074 TGTGGGCTTTAAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
299103 TATGGACTTT-AAAACG-GTGGCACTGACT
1 TGTGGGCTTTGAAAA-GAGTGCCACTGACT
* * *
299131 TGTGGGCTTTAAAAATAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
299160 TGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
299188 TGTGGGCTTTGAAAAAGAGTGCCATTGACT
1 TGTGGGCTTTG-AAAAGAGTGCCACTGACT
*
299218 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
299246 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
299275 TGTGGGCTTTGAAAAGAGTGTCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
299304 TGTGCGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
299332 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
299345 GAGATGAACG
Statistics
Matches: 860, Mismatches: 104, Indels: 57
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.00
28 385 0.45
29 331 0.38
30 60 0.07
31 31 0.04
32 50 0.06
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:298441 original size:57 final size:57
Alignment explanation
Indices: 298356--299344 Score: 1238
Period size: 57 Copynumber: 17.2 Consensus size: 57
298346 CCGACTCGTA
* *
298356 TGGGTTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
298413 TGGGCTTTAAAAAGAGTACCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
298470 TGGGCTTTG-AAAGGGTGCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
298526 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
298583 TGGGCTTTAAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAGGGTGCCAATGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
298640 CATGGGCTCTGAAAA-AGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTG
1 --TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * *
298698 TGGGTTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
* * * * **
298755 TGGGCTTTGAAGAGAGTGCCACCGACTTGTGGGCTTTGAAAAAAGTTGCCACCAACTCGTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG--AAAGGGTGCCACTGACT--TG
* *
298816 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTA
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* *
298873 TGGGCTTTGAAAAGAGTACCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
298930 TGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT--TG
* * *
298991 TGGGCTTTGAAAAGAGTGCGACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAATTA
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * *
299048 TGGGCTTTGAAAAG-GTGCCACTAACTTGTGGGCTTTAAAAAGAGTGCCACTAACTTA
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTG
* * * ** *
299105 TGGACTTT-AAAACG-GTGGCACTGACTTGTGGGCTTTAAAAATAGTGCCACTGATTTG
1 TGGGCTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTG
* * * *
299162 TGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAAGAGTGCCATTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG--AAAGGGTGCCACTGACTTG
* * *
299220 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
* * *
299277 TGGGCTTTGAAAAGAGTGTCACTAACTTGTGCGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
299334 TGGGCTTTGAA
1 TGGGCTTTGAA
299345 GAGATGAACG
Statistics
Matches: 814, Mismatches: 97, Indels: 42
0.85 0.10 0.04
Matches are distributed among these distances:
55 3 0.00
56 102 0.13
57 430 0.53
58 139 0.17
59 60 0.07
60 4 0.00
61 76 0.09
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (57 bp):
TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
Found at i:306493 original size:32 final size:32
Alignment explanation
Indices: 306451--306585 Score: 225
Period size: 32 Copynumber: 4.2 Consensus size: 32
306441 GCTTTGTAGT
* *
306451 GATACTTTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
306483 GATACATTGTATCGATGCAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
306515 GATACATTGTATCGATACAACACTTATTTATC
1 GATACATTGTATCGATACAACACTTATGTATC
306547 GATACATTGTATCGATACAACACTTTATGTATC
1 GATACATTGTATCGATACAACAC-TTATGTATC
306580 GATACA
1 GATACA
306586 AATCATTGAA
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 82 0.85
33 14 0.15
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:306495 original size:13 final size:13
Alignment explanation
Indices: 306477--306565 Score: 61
Period size: 13 Copynumber: 5.9 Consensus size: 13
306467 ACAAAACTTA
306477 TGTATCGATACAT
1 TGTATCGATACAT
306490 TGTATCGATGCAACACTT
1 TGTATCGAT---ACA--T
306508 ATGTATCGATACAT
1 -TGTATCGATACAT
306522 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
306540 ATTTATCGATACAT
1 -TGTATCGATACAT
306554 TGTATCGATACA
1 TGTATCGATACA
306566 ACACTTTATG
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
13 29 0.47
14 2 0.03
16 12 0.19
18 2 0.03
19 17 0.27
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:307418 original size:29 final size:29
Alignment explanation
Indices: 307392--307716 Score: 418
Period size: 29 Copynumber: 11.1 Consensus size: 29
307382 TGTGTTTTTG
* *
307392 AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
* *
307421 AAAGATACCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGG-A
*
307451 AAGGGTGCCACTGACTTGTGGGCTTTGGA
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
**
307480 AAAAATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGG-A
* * *
307510 AAGGGTGCTACTGACTTGTGGGCTTTTGA
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
* *
307539 AAAGATACCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGG-A
*
307569 AAGGGTGCCACTGACTTGTGGGCTTTGGA
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
* **
307598 AAAGATGCCACTGACTTGTGGGCTTT-TC
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
* *
307626 TAGGTTGCCACTGACTTGTGGGCTTTGGA
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
*
307655 AAAGATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGG-A
* *
307685 AAGGGTGCCACTGACTTGTGGGCTTTGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGA
307714 AAG
1 AAG
307717 AAAAAGGTGC
Statistics
Matches: 253, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
28 23 0.09
29 128 0.51
30 102 0.40
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
AAGGATGCCACTGACTTGTGGGCTTTGGA
Found at i:307467 original size:59 final size:59
Alignment explanation
Indices: 307392--307717 Score: 532
Period size: 59 Copynumber: 5.6 Consensus size: 59
307382 TGTGTTTTTG
* * *
307392 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
*
307451 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * *
307510 AAGGGTGCTACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
**
307569 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT--TC
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* *
307626 TAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
307685 AAGGGTGCCACTGACTTGTGGGCTTT-GAAAAGA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
307718 AAAAGGTGCC
Statistics
Matches: 246, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
57 53 0.22
58 7 0.03
59 186 0.76
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (59 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
Found at i:307726 original size:34 final size:34
Alignment explanation
Indices: 307654--307947 Score: 318
Period size: 34 Copynumber: 8.8 Consensus size: 34
307644 TGGGCTTTGG
* *
307654 AAAAGATGCCACTGACTTGTGGGCTTTG----GA
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
* * * *
307684 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
* *
307718 AAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGG
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAA-GA
* * *
307752 AAAAGATGCCATGAAGTTGTGGGC-TTAAAAAGA
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
* *
307785 GAAAAGATGCCACGGAGTTGTGGGC-TTAAAAAGGG
1 -AAAAGATGCCACGGAGTTGTGGGCTTTGAAAA-GA
* *
307820 AAAAGATGCCACAGAGTTGTGGGCTCTGAAAAGA
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
*
307854 AAAAGATGCCACGGAGTTGTGGGCTAT-AAAAGA
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
* *
307887 AAAAGGTGCCACGGGGTTGTGGGCTTTGAAAAGA
1 AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
*
307921 AAAAGGTGCCAC-GAGGTTGTGGGCTTT
1 AAAAGATGCCACGGA-GTTGTGGGCTTT
307948 AGAAGGGTGA
Statistics
Matches: 230, Mismatches: 23, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
30 26 0.11
33 38 0.17
34 160 0.70
35 6 0.03
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (34 bp):
AAAAGATGCCACGGAGTTGTGGGCTTTGAAAAGA
Found at i:309397 original size:11 final size:11
Alignment explanation
Indices: 309379--309515 Score: 115
Period size: 11 Copynumber: 12.5 Consensus size: 11
309369 ATCCAGACCC
309379 TTTTTGTTGTT
1 TTTTTGTTGTT
*
309390 TGTTTGTTTGTT
1 TTTTTG-TTGTT
*
309402 TTTTT-CTGTT
1 TTTTTGTTGTT
309412 TTTTTGTTGTT
1 TTTTTGTTGTT
*
309423 TTTTTTTTGTT
1 TTTTTGTTGTT
309434 TTTTT-TTGTCT
1 TTTTTGTTGT-T
*
309445 CTTTTTTTTGTT
1 -TTTTTGTTGTT
*
309457 TTGTT-TTGTTT
1 TTTTTGTTG-TT
*
309468 TTTTTGTCGTT
1 TTTTTGTTGTT
*
309479 TTTTT-TTCTT
1 TTTTTGTTGTT
309489 TTTTT-TTGTT
1 TTTTTGTTGTT
*
309499 TTGTTT-TTTTT
1 TT-TTTGTTGTT
309510 TTTTTG
1 TTTTTG
309516 CGAAGGACGC
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
10 33 0.31
11 51 0.49
12 17 0.16
13 4 0.04
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (11 bp):
TTTTTGTTGTT
Found at i:309406 original size:1 final size:1
Alignment explanation
Indices: 309400--309514 Score: 77
Period size: 1 Copynumber: 115.0 Consensus size: 1
309390 TGTTTGTTTG
* * * * * * * * * * *
309400 TTTTTTTCTGTTTTTTTGTTGTTTTTTTTTTGTTTTTTTTTGTCTCTTTTTTTTGTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * *
309465 TTTTTTTTGTCGTTTTTTTTTCTTTTTTTTTGTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
309515 GCGAAGGACG
Statistics
Matches: 81, Mismatches: 33, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (1 bp):
T
Found at i:309413 original size:10 final size:10
Alignment explanation
Indices: 309379--309515 Score: 141
Period size: 10 Copynumber: 12.9 Consensus size: 10
309369 ATCCAGACCC
*
309379 TTTTTGTTGT
1 TTTTTTTTGT
309389 TTGTTTGTTTGT
1 TT-TTT-TTTGT
*
309401 TTTTTTCTGT
1 TTTTTTTTGT
309411 TTTTTTGTTGTT
1 TTTTTT-TTG-T
309423 TTTTTTTTGT
1 TTTTTTTTGT
309433 TTTTTTTTGTCT
1 TTTTTTTTG--T
309445 CTTTTTTTTGT
1 -TTTTTTTTGT
*
309456 TTTGTTTTGT
1 TTTTTTTTGT
309466 TTTTTTTGTCGT
1 TTTTTTT-T-GT
*
309478 TTTTTTTTCT
1 TTTTTTTTGT
309488 TTTTTTTTGT
1 TTTTTTTTGT
*
309498 TTTGTTTT-T
1 TTTTTTTTGT
309507 TTTTTTTTG
1 TTTTTTTTG
309516 CGAAGGACGC
Statistics
Matches: 108, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
9 8 0.07
10 54 0.50
11 14 0.13
12 23 0.21
13 9 0.08
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:309457 original size:55 final size:53
Alignment explanation
Indices: 309379--309514 Score: 163
Period size: 55 Copynumber: 2.5 Consensus size: 53
309369 ATCCAGACCC
* * *
309379 TTTTTGTTG-TTTGTTTGTTTGTTTTTTTCTG-TTTTTTTGTTGTTTTTTTTTTGT
1 TTTTTTTTGTTTTGTTT-TTTGTTTTTTT-TGTTTTTTTTGTCG-TTTTTTTTTCT
309433 TTTTTTTTGTCTCTT-TTTTTTGTTTTGTTTTGTTTTTTTTGTCGTTTTTTTTTCT
1 TTTTTTTTGT-T-TTGTTTTTTGTTTT-TTTTGTTTTTTTTGTCGTTTTTTTTTCT
309488 TTTTTTTTGTTTTGTTTTTT-TTTTTTT
1 TTTTTTTTGTTTTGTTTTTTGTTTTTTT
309515 GCGAAGGACG
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
52 3 0.04
53 6 0.08
54 15 0.21
55 30 0.41
56 17 0.23
57 2 0.03
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (53 bp):
TTTTTTTTGTTTTGTTTTTTGTTTTTTTTGTTTTTTTTGTCGTTTTTTTTTCT
Found at i:309459 original size:42 final size:40
Alignment explanation
Indices: 309379--309513 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 40
309369 ATCCAGACCC
* *
309379 TTTTTGTTGTTTGTTTGTTTGT-TTTTTTCTGTTTTTTTGTTGTT
1 TTTTTTTTGTTT-TTT-TTTGTCTTTTTT-T-TTGTTTTGTT-TT
309423 TTTTTTTTGTTTTTTTTTGTCTCTTTTTTTTGTTTTGTTTT
1 TTTTTTTTGTTTTTTTTTGTCT-TTTTTTTTGTTTTGTTTT
309464 GTTTTTTTTGTCGTTTTTTTT-TCTTTTTTTTTGTTTTGTTTT
1 -TTTTTTTTGT--TTTTTTTTGTCTTTTTTTTTGTTTTGTTTT
309506 TTTTTTTT
1 TTTTTTTT
309514 TGCGAAGGAC
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
41 10 0.12
42 42 0.50
43 8 0.10
44 24 0.29
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.84
Consensus pattern (40 bp):
TTTTTTTTGTTTTTTTTTGTCTTTTTTTTTGTTTTGTTTT
Found at i:309474 original size:32 final size:31
Alignment explanation
Indices: 309388--309515 Score: 131
Period size: 32 Copynumber: 4.1 Consensus size: 31
309378 CTTTTTGTTG
309388 TTTG-TTTG-TTTGTTTTTTTCTGT-TTTTTT
1 TTTGTTTTGTTTTGTTTTTTT-TGTCTTTTTT
* *
309417 GTTGTTTTTTTTTTGTTTTTTTTTGTCTCTTTTT
1 TTTG-TTTTGTTTTG-TTTTTTTTGTCT-TTTTT
309451 TTTGTTTTGTTTTGTTTTTTTTGTCGTTTTTT
1 TTTGTTTTGTTTTGTTTTTTTTGTC-TTTTTT
* * *
309483 TTTCTTTTTTTTTGTTTTGTTT-T-TTTTTT
1 TTTGTTTTGTTTTGTTTTTTTTGTCTTTTTT
309512 TTTG
1 TTTG
309516 CGAAGGACGC
Statistics
Matches: 84, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
29 12 0.14
31 4 0.05
32 42 0.50
33 18 0.21
34 8 0.10
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (31 bp):
TTTGTTTTGTTTTGTTTTTTTTGTCTTTTTT
Found at i:323505 original size:52 final size:52
Alignment explanation
Indices: 323357--323485 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
323347 CGAAATATGA
323357 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
323409 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATTTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
323461 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
323486 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:323512 original size:13 final size:13
Alignment explanation
Indices: 323494--323518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323484 CAAAGATCAG
323494 TGTATCGATACAA
1 TGTATCGATACAA
323507 TGTATCGATACA
1 TGTATCGATACA
323519 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:323608 original size:13 final size:13
Alignment explanation
Indices: 323590--323614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323580 ACAAAACTTA
323590 TGTATCGATACAT
1 TGTATCGATACAT
323603 TGTATCGATACA
1 TGTATCGATACA
323615 AATCGTTGAA
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:333125 original size:20 final size:20
Alignment explanation
Indices: 333100--333196 Score: 140
Period size: 20 Copynumber: 4.8 Consensus size: 20
333090 AATTTTAACT
333100 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
333120 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
* * * *
333140 GAATGTATCGATATATTCAT
1 AAATGTATCGATACATTGAA
*
333160 ACATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
*
333180 TAATGTATCGATACATT
1 AAATGTATCGATACATT
333197 TGGGTACTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTGAA
Done.