Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold146
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1000955
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 102963 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:4778 original size:2 final size:2
Alignment explanation
Indices: 4773--4825 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4763 AAAGTCTATA
4773 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4815 CT CT CT CT CT C
1 CT CT CT CT CT C
4826 GTCACGAATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:7247 original size:5 final size:5
Alignment explanation
Indices: 7237--7263 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
7227 TGTAAACTTT
7237 TTCAA TTCAA TTCAA TTCAA TTCAA TT
1 TTCAA TTCAA TTCAA TTCAA TTCAA TT
7264 TATTTCACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (5 bp):
TTCAA
Found at i:7270 original size:15 final size:15
Alignment explanation
Indices: 7236--7270 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7226 TTGTAAACTT
7236 TTTCAATTCAATTCA
1 TTTCAATTCAATTCA
* *
7251 ATTCAATTCAATTTA
1 TTTCAATTCAATTCA
7266 TTTCA
1 TTTCA
7271 CTCAAACCGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTCAATTCAATTCA
Found at i:7461 original size:9 final size:9
Alignment explanation
Indices: 7447--7471 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7437 ATAAATAAAC
7447 AAGTTTTTT
1 AAGTTTTTT
7456 AAGTTTTTT
1 AAGTTTTTT
7465 AAGTTTT
1 AAGTTTT
7472 AAAGTAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (9 bp):
AAGTTTTTT
Found at i:10708 original size:2 final size:2
Alignment explanation
Indices: 10701--10748 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
10691 NNNNNNNNNN
10701 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10743 TC TC TC
1 TC TC TC
10749 AACCGTTACT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17132 original size:2 final size:2
Alignment explanation
Indices: 17125--17162 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
17115 TAATTTTTAC
*
17125 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA TA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17163 TTTATTAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:19088 original size:2 final size:2
Alignment explanation
Indices: 19081--19130 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
19071 TGATCGTTAT
19081 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19123 GA GA GA GA
1 GA GA GA GA
19131 TTGTTTTAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19580 original size:65 final size:65
Alignment explanation
Indices: 19350--19683 Score: 404
Period size: 65 Copynumber: 5.1 Consensus size: 65
19340 AATAGTTTTC
* * * * *
19350 ATTTCAAGTAAGGGGAACA-GAAGTATGCCTAACAATAAAGTATTCTACACTGTTTGTGATGTTT
1 ATTTCAAGTAAAGAGAA-AGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTT
19414 G
65 G
* *
19415 ATTTCAAGTAAAGAGAAAGGAAGCA-GCCTATCAATGAAGTATTCTACACTGTTTGTGATGTTTG
1 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
*
19479 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTATCAATGAAGTATTATACACTGTTTGTGATGTTTT
1 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATG-TTT
19544 G
65 G
* * * * **
19545 ATTTCTAGCAAAGAGAAA-AAAGTATGTGTAACAATGAAGTACATGTATTCTACACTGTTTGTGA
1 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGT--AT-TA---TACACTGTTTGTGA
19609 TGTTTG
60 TGTTTG
* * ** *
19615 ATTTCAAGTAAAGAGAATGGAATCAAACTTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
1 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
19680 ATTT
1 ATTT
19684 AAAGATTGAT
Statistics
Matches: 236, Mismatches: 23, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
64 63 0.27
65 95 0.40
66 20 0.08
67 2 0.01
68 4 0.02
69 2 0.01
70 19 0.08
71 31 0.13
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (65 bp):
ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
Found at i:19621 original size:136 final size:129
Alignment explanation
Indices: 19350--19683 Score: 411
Period size: 136 Copynumber: 2.5 Consensus size: 129
19340 AATAGTTTTC
* * * * *
19350 ATTTCAAGTAAGGGGAACA-GAAGTATGCCTAACAATAAAGTATTCTACACTGTTTGTGATGTTT
1 ATTTCAAGTAAAGAGAA-AGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTT
* * *
19414 GATTTCAAGTAAAGAGAAAGGAAGCAGCCTATCAATGAAGTATTCTACACTGTTTGTGATGTTTG
65 GATTTCAAGCAAAGAGAAAGAAAGCAGCCTAACAATGAAGTATTCTACACTGTTTGTGATGTTTG
*
19479 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTATCAATGAAGTATTATACACTGTTTGTGATGTTTT
1 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATG-TTT
* * **
19544 GATTTCTAGCAAAGAGAAA-AAAGTATGTGTAACAATGAAGTACATGTATTCTACACTGTTTGTG
65 GATTTCAAGCAAAGAGAAAGAAAGCA-GCCTAACAAT---G-A-A-GTATTCTACACTGTTTGTG
19608 ATGTTTG
123 ATGTTTG
* * ** *
19615 ATTTCAAGTAAAGAGAATGGAATCAAACTTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
1 ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
19680 ATTT
66 ATTT
19684 AAAGATTGAT
Statistics
Matches: 177, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
128 1 0.01
129 57 0.32
130 27 0.15
133 1 0.01
134 1 0.01
135 9 0.05
136 81 0.46
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (129 bp):
ATTTCAAGTAAAGAGAAAGGAAGCATGCCTAACAATGAAGTATTATACACTGTTTGTGATGTTTG
ATTTCAAGCAAAGAGAAAGAAAGCAGCCTAACAATGAAGTATTCTACACTGTTTGTGATGTTTG
Found at i:19756 original size:2 final size:2
Alignment explanation
Indices: 19749--19807 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
19739 CAGAAATAAA
19749 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19791 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
19808 TTCTGACACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24054 original size:19 final size:19
Alignment explanation
Indices: 24021--24057 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24011 GGGTCCAGAG
24021 ATTGTCTTAAGGACTTAAA
1 ATTGTCTTAAGGACTTAAA
24040 ATTGTACTTAA-GACTTAA
1 ATTGT-CTTAAGGACTTAA
24058 GGTCTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
ATTGTCTTAAGGACTTAAA
Found at i:28538 original size:2 final size:2
Alignment explanation
Indices: 28531--28564 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28521 ATTTTAACAA
28531 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28565 GTTGTTTTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41937 original size:2 final size:2
Alignment explanation
Indices: 41930--41957 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41920 NNNNNNNNNN
41930 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
41958 AAAACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47554 original size:2 final size:2
Alignment explanation
Indices: 47549--47596 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
47539 GTATATACAT
47549 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47591 TC TC TC
1 TC TC TC
47597 AGAGAAATAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:52233 original size:109 final size:109
Alignment explanation
Indices: 52042--52239 Score: 378
Period size: 109 Copynumber: 1.8 Consensus size: 109
52032 NNNNNNNNNN
52042 TATAGCTACATGTTCGTCTTAACTATATAATAGTTTATTGCTAAATGTAGCAAAATCAATGCTAG
1 TATAGCTACATGTTCGTCTTAACTATATAATAGTTTATTGCTAAATGTAGCAAAATCAATGCTAG
52107 AATTTTAAGGAGATCATCAAGAGGTATATATATATATATAAAGC
66 AATTTTAAGGAGATCATCAAGAGGTATATATATATATATAAAGC
*
52151 TATAGCTACATGTTCGTCTTAACTATATAATAGTTTATTGCTACATGTAGCAAAATCAATGCTAG
1 TATAGCTACATGTTCGTCTTAACTATATAATAGTTTATTGCTAAATGTAGCAAAATCAATGCTAG
*
52216 AATTTTAAGGTGATCATCAAGAGG
66 AATTTTAAGGAGATCATCAAGAGG
52240 AAAATGAAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 87 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (109 bp):
TATAGCTACATGTTCGTCTTAACTATATAATAGTTTATTGCTAAATGTAGCAAAATCAATGCTAG
AATTTTAAGGAGATCATCAAGAGGTATATATATATATATAAAGC
Found at i:54528 original size:37 final size:37
Alignment explanation
Indices: 54478--54553 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
54468 TTTCATGTCC
54478 TTAATCAAACGTAATTAATACAAAAAAT-TGTCATCAA
1 TTAATCAAACGTAATTAATAC-AAAAATCTGTCATCAA
* *
54515 TTAATCAAACGTAATTTATACAAAAGTCTGTCATCAA
1 TTAATCAAACGTAATTAATACAAAAATCTGTCATCAA
54552 TT
1 TT
54554 TCTTGTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 5 0.14
37 31 0.86
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (37 bp):
TTAATCAAACGTAATTAATACAAAAATCTGTCATCAA
Found at i:54992 original size:25 final size:23
Alignment explanation
Indices: 54942--54992 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
54932 TTTGGGTGTA
* *
54942 TTTTTTTGTTTTTGTTTGTTTTG
1 TTTTTTTGTTTTTGTTTGTATAG
*
54965 TTTTTTTGTTTTTAATTTTGTATAG
1 TTTTTTTGTTTTT--GTTTGTATAG
54990 TTT
1 TTT
54993 ACTAAAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78
Consensus pattern (23 bp):
TTTTTTTGTTTTTGTTTGTATAG
Found at i:60823 original size:59 final size:59
Alignment explanation
Indices: 60751--60868 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
60741 AACTTTGTGG
60751 CTGTGACAATATGTGTTAGTAAGATTCTCTCCTGTAGGGCGGAATCCATGTGGTTCAGT
1 CTGTGACAATATGTGTTAGTAAGATTCTCTCCTGTAGGGCGGAATCCATGTGGTTCAGT
60810 CTGTGACAATATGTGTTAGTAAGATTCTCTCCTGTAGGGCGGAATCCATGTGGTTCAGT
1 CTGTGACAATATGTGTTAGTAAGATTCTCTCCTGTAGGGCGGAATCCATGTGGTTCAGT
60869 TGCTGGACTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (59 bp):
CTGTGACAATATGTGTTAGTAAGATTCTCTCCTGTAGGGCGGAATCCATGTGGTTCAGT
Found at i:67447 original size:22 final size:22
Alignment explanation
Indices: 67217--67627 Score: 295
Period size: 22 Copynumber: 18.9 Consensus size: 22
67207 GTCACAAAAA
* *
67217 GGTGTCTGAAAGGTAACTAACA-
1 GGTGACTGAAATGTAACTAA-AG
* * *
67239 AGTGATTGAAAGGTAACTAAAG
1 GGTGACTGAAATGTAACTAAAG
* *
67261 GATGACTGAAAGGTAACTAATA-
1 GGTGACTGAAATGTAACTAA-AG
* * *
67283 GGTGATTG-AAGGAAACTAAAG
1 GGTGACTGAAATGTAACTAAAG
* *
67304 GGTGACTG-AATGCAAACAAAAG
1 GGTGACTGAAATG-TAACTAAAG
* * *
67326 GATGACTGAGATGTATCTAAAG
1 GGTGACTGAAATGTAACTAAAG
* **
67348 GGTGACTG-AATGGAAACTTGAG
1 GGTGACTGAAAT-GTAACTAAAG
67370 GGTGACTGAAATGTAACTAAAG
1 GGTGACTGAAATGTAACTAAAG
* * *
67392 GGTGACTG-AATGGAAACTTAGG
1 GGTGACTGAAAT-GTAACTAAAG
67414 GGTGACTGAAATGTAACTAAAG
1 GGTGACTGAAATGTAACTAAAG
* *
67436 GGTGACTGAAATGAAAATAAAG
1 GGTGACTGAAATGTAACTAAAG
* * *
67458 GGTAACTAAAATGTAGCTAAAG
1 GGTGACTGAAATGTAACTAAAG
* * * * *
67480 GGTGACAGACAGGCATCTAAAG
1 GGTGACTGAAATGTAACTAAAG
* *
67502 GGTCACT---ATGTAACTAAAA
1 GGTGACTGAAATGTAACTAAAG
* * *
67521 GGAGACTGAGACGTAACTACAA-
1 GGTGACTGAAATGTAACTA-AAG
* *
67543 GGTGACCGAAAGGTAACTAAAG
1 GGTGACTGAAATGTAACTAAAG
* * *
67565 GCTGACT-AAACGGTAACTAGAG
1 GGTGACTGAAA-TGTAACTAAAG
* *
67587 GTTGACTGAAATGTAATTAAAG
1 GGTGACTGAAATGTAACTAAAG
67609 GGTGACTGAAATGTAACTA
1 GGTGACTGAAATGTAACTA
67628 CATTTGTAAA
Statistics
Matches: 305, Mismatches: 68, Indels: 32
0.75 0.17 0.08
Matches are distributed among these distances:
19 13 0.04
20 1 0.00
21 31 0.10
22 245 0.80
23 15 0.05
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GGTGACTGAAATGTAACTAAAG
Found at i:67625 original size:44 final size:44
Alignment explanation
Indices: 67240--67673 Score: 294
Period size: 44 Copynumber: 9.8 Consensus size: 44
67230 TAACTAACAA
* * * * *
67240 GTGATTGAAAGGTAACTAAAGGATGACTGAAAGGTAACTAATA-G
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATGAAACTAA-AGG
* * * *
67284 GTGATTG-AAGGAAACTAAAGGGTGACTG-AATGCAAACAAAAGG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATG-AAACTAAAGG
* * * **
67327 ATGACTGAGATGTATCTAAAGGGTGACTG-AATGGAAACTTGAGG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAAT-GAAACTAAAGG
* *
67371 GTGACTGAAATGTAACTAAAGGGTGACTG-AATGGAAACTTAGGG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAAT-GAAACTAAAGG
*
67415 GTGACTGAAATGTAACTAAAGGGTGACTGAAATGAAAATAAAGG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATGAAACTAAAGG
* * * * * * * *
67459 GTAACTAAAATGTAGCTAAAGGGTGACAGACAGGCATCTAAAGG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATGAAACTAAAGG
* * * * * *
67503 GTCACT---ATGTAACTAAAAGGAGACTGAGACGTAACTACAA-G
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATGAAACTA-AAGG
* * * * * *
67544 GTGACCGAAAGGTAACTAAAGGCTGACT-AAACGGTAACTAGAGG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAA-TGAAACTAAAGG
* * *
67588 TTGACTGAAATGTAATTAAAGGGTGACTGAAATGTAACTACATTTGTAAATG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATG-AA--AC-----TAAAGG
* *
67640 GTGACTGAAAGGAAACTAAAGGGTGACTGAAATG
1 GTGACTGAAATGTAACTAAAGGGTGACTGAAATG
67674 TAACAGCAAG
Statistics
Matches: 308, Mismatches: 62, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
41 28 0.09
42 6 0.02
43 33 0.11
44 197 0.64
45 8 0.03
47 2 0.01
52 34 0.11
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.21
Consensus pattern (44 bp):
GTGACTGAAATGTAACTAAAGGGTGACTGAAATGAAACTAAAGG
Found at i:69507 original size:2 final size:2
Alignment explanation
Indices: 69500--69582 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
69490 TTCTCTACAT
69500 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
69542 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
69583 GGGGGTAGGT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:83094 original size:97 final size:97
Alignment explanation
Indices: 82928--83128 Score: 393
Period size: 97 Copynumber: 2.1 Consensus size: 97
82918 AATTTAAAAC
*
82928 ACTAAAATTTGTGCAGTCTTAAAATTCACCGCTGACAACGAGGAAAAAAGGGGCAAAAATAAAAC
1 ACTAAGATTTGTGCAGTCTTAAAATTCACCGCTGACAACGAGGAAAAAAGGGGCAAAAATAAAAC
82993 AGGGACGAATAATTGATTATATAAGATCAATG
66 AGGGACGAATAATTGATTATATAAGATCAATG
83025 ACTAAGATTTGTGCAGTCTTAAAATTCACCGCTGACAACGAGGAAAAAAGGGGCAAAAATAAAAC
1 ACTAAGATTTGTGCAGTCTTAAAATTCACCGCTGACAACGAGGAAAAAAGGGGCAAAAATAAAAC
83090 AGGGACGAATAATTGATTATATAAGATCAATG
66 AGGGACGAATAATTGATTATATAAGATCAATG
83122 ACTAAGA
1 ACTAAGA
83129 AAGATACCAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 103 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.21
Consensus pattern (97 bp):
ACTAAGATTTGTGCAGTCTTAAAATTCACCGCTGACAACGAGGAAAAAAGGGGCAAAAATAAAAC
AGGGACGAATAATTGATTATATAAGATCAATG
Found at i:85263 original size:177 final size:177
Alignment explanation
Indices: 85067--85979 Score: 1105
Period size: 177 Copynumber: 5.2 Consensus size: 177
85057 GGGTCCTAAA
* * * *
85067 TTTCAGATGCTGAAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * *
85132 GATAGCAATATCTAAGTTACTCCTGGTCCTAACTTCACCAAACTTGCATGGATGGTGTGTCTTAT
66 GATAGCAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTAT
* * * *
85197 GATACTGATCCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG
131 GATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* *
85244 -TTCTGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTT
1 TTTC-GGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTC
* * * *
85308 TGATAGCAATGTCTAAGTTACTGCTGGTCCGT-ACTTCACCAAACTTGCATGGATGGTGTGTCTT
65 TGATAGCAATATCTTAGTTACTACTGGTCC-TAACTTCACCAAACTTGCATGGATGGTGCGTCTT
* * * *
85372 ATGTTACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCTATTGG
129 ATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* **
85421 TTTCGGATGCTGGAGGTGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * * *
85486 GAT-GATAATAACTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGTTGGTGCGTCCTA
66 GATAG-CAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTA
*
85550 TGATACTGGTGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
130 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
*
85598 TTTCGGATG-TGGAGGAGGTTAA-GTTTTTGGAGCTGGTTAAAGTTTTT-TGAGCAGGTGCCCTC
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGT-TGCAGGTGCCCTC
* * * * * **
85660 T-A-A-CGATTATATCTTAGCTACTCCTGGTCCAAACTTCATCAAATTTGTGTGGATGGTGCGTC
65 TGATAGC-A--ATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTC
* *
85722 TTATTATACTGATGCTCCTGA-ATGGCTTGAATGCTGAATCTGAGCCATAGG
127 TTATGATACTGATGCACCTGACA-GGCTTGAATGCTGAATCTGAGCCATAGG
** ***
85773 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGAAACAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * * * *
85838 GAT-G-ATGATATCTTAGTTATTACTTGTCCTAGCTTCACCAGACTTCCATGGATGGTGCATTTT
66 GATAGCA--ATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTT
* *
85901 ATGATACTGATGCACCTGACAGGCTTTAATGCT-AAGTCTTAGCCATAGG
129 ATGATACTGATGCACCTGACAGGCTTGAATGCTGAA-TCTGAGCCATAGG
* ** *
85950 TTTCTGATGCTGGATAAGTTTAAGGTTTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTT
85980 TTAACAGGTC
Statistics
Matches: 644, Mismatches: 73, Indels: 38
0.85 0.10 0.05
Matches are distributed among these distances:
173 1 0.00
174 3 0.00
175 135 0.21
176 32 0.05
177 467 0.73
178 6 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (177 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
GATAGCAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTAT
GATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGG
Found at i:85301 original size:19 final size:19
Alignment explanation
Indices: 85254--85293 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
85244 TTCTGGATGC
* *
85254 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
85273 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
85292 TG
1 TG
85294 TTGCAGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:85628 original size:18 final size:19
Alignment explanation
Indices: 85607--85653 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
85597 GTTTCGGATG
*
85607 TGGAGGAGGTT-AAGTTTT
1 TGGAGCAGGTTAAAGTTTT
*
85625 TGGAGCTGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
*
85644 TTGAGCAGGT
1 TGGAGCAGGT
85654 GCCCTCTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.21, C:0.04, G:0.36, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:85796 original size:352 final size:354
Alignment explanation
Indices: 85067--85979 Score: 1157
Period size: 352 Copynumber: 2.6 Consensus size: 354
85057 GGGTCCTAAA
* * ** * *
85067 TTTCAGATGCTGAAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * *
85132 GAT-AGCAATATCTAAGTTACTCCTGGTCCTAACTTCACCAAACTTGCATGGATGGTGTGTCTTA
66 GATGA-TAATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGCATGGATGGTGCGTCTTA
* * * *
85196 TGATACTGATCCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG-TTCTGGATGCTGGAGG
130 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTC-GGATGCTGGAGG
* * *
85260 AGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATGTCTAAG
194 AGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTAGCAGGTGCCCTCTGATAGCAATATCTAAG
* * ** *
85325 TTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGTTACTGATGCACCAG
259 CTACTCCTGGTCCAAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGTTACTGATGCACCAG
* *
85390 ACAGGCTTGAATGCTGAATCTGAGCTATTGG
324 ACAGGCTTGAATGCTGAATCTGAGCCATAGG
*
85421 TTTCGGATGCTGGAGGTGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * *
85486 GATGATAATAACTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGTTGGTGCGTCCTAT
66 GATGATAATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGCATGGATGGTGCGTCTTAT
*
85551 GATACTGGTGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATG-TGGAGGAG
131 GATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAG
* *
85615 GTTAA-GTTTTTGGAGCTGGTTAAAGTTTTT-TGAGCAGGTGCCCTCT-A-A-CGATTATATCTT
196 GTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGT-AGCAGGTGCCCTCTGATAGC-A--ATATCTA
* * ** *
85675 AGCTACTCCTGGTCCAAACTTCATCAAATTTGTGTGGATGGTGCGTCTTAT-TATACTGATGCTC
257 AGCTACTCCTGGTCCAAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGT-TACTGATGCAC
*
85739 CTGA-ATGGCTTGAATGCTGAATCTGAGCCATAGG
321 CAGACA-GGCTTGAATGCTGAATCTGAGCCATAGG
***
85773 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGAAACAGGTGCCCTCT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
* * * * * * *
85838 GATGATGATATCTTAGTTATTACTTGTCC-TAGCTTCACCAGACTTCCATGGATGGTGCATTTTA
66 GATGATAATATCTTAGTTACTACTGGTCCTTA-CTTCACCAAACTTGCATGGATGGTGCGTCTTA
* * * **
85902 TGATACTGATGCACCTGACAGGCTTTAATGCT-AAGTCTTAGCCATAGGTTTCTGATGCTGGATA
130 TGATACTGATGCACCTGACAGGCTTGAATGCTGAA-TCTGAGCCATAGGTTTCGGATGCTGGAGG
*
85966 AGTTTAAGGTTTTT
194 AGGTTAAGGTTTTT
85980 TTAACAGGTC
Statistics
Matches: 486, Mismatches: 61, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
349 1 0.00
350 2 0.00
351 8 0.02
352 283 0.58
353 23 0.05
354 165 0.34
355 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (354 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
GATGATAATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGCATGGATGGTGCGTCTTAT
GATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAG
GTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTAGCAGGTGCCCTCTGATAGCAATATCTAAGCT
ACTCCTGGTCCAAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGTTACTGATGCACCAGAC
AGGCTTGAATGCTGAATCTGAGCCATAGG
Found at i:97220 original size:2 final size:2
Alignment explanation
Indices: 97213--97252 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
97203 AAACAAAAAC
97213 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
97253 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:103110 original size:2 final size:2
Alignment explanation
Indices: 103103--103164 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
103093 CGCACCACTC
103103 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
103144 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
103165 TGGCGTAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:103952 original size:11 final size:11
Alignment explanation
Indices: 103936--103962 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
103926 TTTGTTTATT
103936 TTAAATGCACC
1 TTAAATGCACC
103947 TTAAATGCACC
1 TTAAATGCACC
103958 TTAAA
1 TTAAA
103963 AAATATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (11 bp):
TTAAATGCACC
Found at i:105505 original size:6 final size:6
Alignment explanation
Indices: 105494--105551 Score: 75
Period size: 6 Copynumber: 9.7 Consensus size: 6
105484 TTTGGTTGTT
*
105494 TTTTTG TTTTTG TTTTTTG TTTTT- TTTTTG TTTTTGG GTTTT- TTTTTG
1 TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTT-G TTTTTG TTTTTG
105542 TTTTTG TTTT
1 TTTTTG TTTT
105552 ATTAACGAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
5 9 0.20
6 26 0.57
7 11 0.24
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:105524 original size:24 final size:24
Alignment explanation
Indices: 105492--105551 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
105482 AATTTGGTTG
*
105492 TTTTTTTGTTTTT-GTTTTTTGTTT
1 TTTTTTTGTTTTTGGGTTTTT-TTT
105516 TTTTTTTGTTTTTGGGTTTTTTTT
1 TTTTTTTGTTTTTGGGTTTTTTTT
*
105540 TGTTTTTGTTTT
1 TTTTTTTGTTTT
105552 ATTAACGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (24 bp):
TTTTTTTGTTTTTGGGTTTTTTTT
Found at i:122796 original size:21 final size:21
Alignment explanation
Indices: 122766--122828 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 21
122756 ATATTTTCAC
*
122766 CTCGTAATTACGAGAAAAGAT
1 CTCGTTATTACGAGAAAAGAT
** * ***
122787 CTCGTTATTAATAGTTATTTAT
1 CTCGTTATTACGAG-AAAAGAT
122809 CTCGTTATTACGAGAAAAGA
1 CTCGTTATTACGAGAAAAGA
122829 CACATAGCAT
Statistics
Matches: 28, Mismatches: 13, Indels: 2
0.65 0.30 0.05
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
CTCGTTATTACGAGAAAAGAT
Found at i:134787 original size:24 final size:25
Alignment explanation
Indices: 134760--134810 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
134750 ATTACAGAAG
134760 TATTCATG-AAAA-CTTCTGTATTAT
1 TATTCATGAAAAATCTT-TGTATTAT
**
134784 TATTGTTGAAAAATCTTTGTATTAT
1 TATTCATGAAAAATCTTTGTATTAT
134809 TA
1 TA
134811 CAGGACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.26
25 14 0.61
26 3 0.13
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (25 bp):
TATTCATGAAAAATCTTTGTATTAT
Found at i:140948 original size:16 final size:16
Alignment explanation
Indices: 140927--140958 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
140917 TACCTTGTGT
140927 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
140943 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
140959 ATAACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38
Consensus pattern (16 bp):
GTCTGTCTGTCCGTCC
Found at i:141353 original size:164 final size:166
Alignment explanation
Indices: 140984--141383 Score: 630
Period size: 167 Copynumber: 2.4 Consensus size: 166
140974 GTCGCATTTA
*
140984 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTAT-AGGCATGCCATA
** *
141048 TTATGGGATATATTTTTGTACTAATCAAACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGAC-TTGCTTATTT
*
141113 TTTAACCAAAATTTTCAAACAAATTTTTGTCAAAGAAT
129 TTTAACAAAAATTTTCAAACAAATTTTTGTCAAAGAAT
* *
141151 TCTCAGCAACTATTTATCGCAGATGCTTGAATTTTTTACACAATATTTGTATAGGCAT-CGCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGC-CATA
* *
141215 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGAC-TGTTTA-TTT
65 TCGTGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTGCTTATTTT
*
141278 TTAGCAAAAATTTTCAAA-AAATTTTTTGTCAAAGAAT
130 TTAACAAAAATTTTCAAACAAA-TTTTTGTCAAAGAAT
*
141315 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
141380 CGTG
66 CGTG
141384 NNNNNNNNNN
Statistics
Matches: 216, Mismatches: 13, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
163 3 0.01
164 98 0.45
165 6 0.03
166 1 0.00
167 107 0.50
168 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTGCTTATTTTT
TAACAAAAATTTTCAAACAAATTTTTGTCAAAGAAT
Found at i:148542 original size:21 final size:22
Alignment explanation
Indices: 148518--148566 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
148508 GGGACTCTTG
*
148518 TTATTGTAGGTTAATTTGTG-T
1 TTATTGTAAGTTAATTTGTGTT
*
148539 TTATTGTAAGTTACTTTGTGTT
1 TTATTGTAAGTTAATTTGTGTT
148561 TTATTG
1 TTATTG
148567 CAGAAGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.59
Consensus pattern (22 bp):
TTATTGTAAGTTAATTTGTGTT
Found at i:150890 original size:2 final size:2
Alignment explanation
Indices: 150883--150924 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
150873 GCAATATAGT
150883 AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
150924 A
1 A
150925 TGATGATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:150931 original size:3 final size:3
Alignment explanation
Indices: 150923--150956 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
150913 GAGAGAGAGA
150923 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
150957 CATGCATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:158988 original size:14 final size:14
Alignment explanation
Indices: 158969--159003 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
158959 CAGCATTTTG
*
158969 ACTGTTGGACTGGA
1 ACTGTTAGACTGGA
*
158983 ACTGTTAGATTGGA
1 ACTGTTAGACTGGA
158997 ACTGTTA
1 ACTGTTA
159004 AAATCGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (14 bp):
ACTGTTAGACTGGA
Found at i:178641 original size:41 final size:41
Alignment explanation
Indices: 178176--178634 Score: 659
Period size: 41 Copynumber: 11.2 Consensus size: 41
178166 TACCTTACCG
* *
178176 TGACATTGAAATTTGTTACATTATTGGCTGTCAGTTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
* *
178217 TGACATTGAGATTTATTACATTATTGGCTGTCAGTTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
* * *
178258 TGATATTGAGATTTTGTAACATTATTGGCTGTCA-TCTATCCA
1 TGACATTGAGA-TTTGTTACATTATTGGCTGTCACT-TCTCCA
* *
178300 TGATATTGAGATTTGTTACATTATTGGCTGTCACCTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
* * **
178341 TGACATTGAGATGTGTTACATTATTGGCTGTCAGTTCTCTG
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
*
178382 TGACATTGAGATTTGTTACATTATTGGCTGTCAGTTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
*
178423 TGACATTGAGATCTGTTACATTATTGGCTGTCACTTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
* * * *
178464 TGACATTGAGATCTGTTACATAATTGGCTGTCGCCTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
* * *
178505 TGACATTGAGATTTGTTACATTATTGCCTGTCACCTCTCCG
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
*
178546 TGACATTGAGATTTGTTACATTATTGCCTGTCACTTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
* *
178587 TGACATTGAGATTTGTTACATTATTGCCTGTCACCTCTCCA
1 TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
*
178628 TAACATT
1 TGACATT
178635 ATGATTTCTC
Statistics
Matches: 383, Mismatches: 32, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
41 347 0.91
42 36 0.09
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (41 bp):
TGACATTGAGATTTGTTACATTATTGGCTGTCACTTCTCCA
Found at i:178788 original size:55 final size:54
Alignment explanation
Indices: 178704--179490 Score: 1028
Period size: 55 Copynumber: 14.4 Consensus size: 54
178694 TTCTCTGTTG
* * *
178704 TTGATATCTATGATGTGATTGGTTGTCATTTCTTTGTTGTTGATTACAGGTGATT
1 TTGATATCTGTGATGTGATT-GTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* * * * *
178759 TTGATATATGTGATATGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATA
1 TTGATATCTGTGATGTGATTG-TTGTCATTTCTCTGTTGTTGATTACAGGTGATA
178814 TTGATATCTGTGATGTGATTTGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
1 TTGATATCTGTGATGTGA-TTGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
*
178869 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATT
1 TTGATATCTGTGATGTGATT-GTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* * * *
178924 TTGATATATGTGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATA
1 TTGATATCTGTGATGTGATTG-TTGTCATTTCTCTGTTGTTGATTACAGGTGATA
*
178979 TTGATATCTGTGATGTGATTTGTTGTCATTTCTCTTTTGTTGATTACAGGTGATA
1 TTGATATCTGTGATGTGA-TTGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
*
179034 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATT
1 TTGATATCTGTGATGTGATT-GTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* * *
179089 TTGATATCTGTGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATA
1 TTGATATCTGTGATGTGATTG-TTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* * *
179144 TTGAAATCTGTGATGTGATTTGTTGTCATTTATCTGTTGTTGATTATAGGTGATA
1 TTGATATCTGTGATGTGA-TTGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* * * **
179199 TTGATATCTATGATGTGATTGTTTGTCATTTCTTTTTTGTTGATTACAAATGATA
1 TTGATATCTGTGATGTGATTG-TTGTCATTTCTCTGTTGTTGATTACAGGTGATA
**
179254 TTGATATCTGTGATGTGATTGTTTGTCATTTCTCTGTTGTTGATTACAAATGATA
1 TTGATATCTGTGATGTGATTG-TTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* * * * * *
179309 TTGATATATGTGACGTGGTTTATTGTCATTTATCTGGTGTT-ATATACAGGTGATA
1 TTGATATCTGTGATGT-GATTGTTGTCATTTCTCTGTTGTTGAT-TACAGGTGATA
* * **
179364 TCGATATCTGTGAT-TG-TCT-TT-TCATTTCTCTGTTGTTGATTGCAAATGATA
1 TTGATATCTGTGATGTGAT-TGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
* *
179415 TTGATATCTGTGATGTGATTGATTTTCATTTCTCTGTTGCTT-CTTACAGGTGATA
1 TTGATATCTGTGATGTGATTG-TTGTCATTTCTCTGTTG-TTGATTACAGGTGATA
179470 TTGATATCTGTGATGTGATTG
1 TTGATATCTGTGATGTGATTG
179491 GGTGTCACCT
Statistics
Matches: 645, Mismatches: 68, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
51 35 0.05
52 8 0.01
53 3 0.00
54 15 0.02
55 570 0.88
56 14 0.02
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.49
Consensus pattern (54 bp):
TTGATATCTGTGATGTGATTGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
Found at i:178976 original size:165 final size:165
Alignment explanation
Indices: 178704--179489 Score: 1201
Period size: 165 Copynumber: 4.8 Consensus size: 165
178694 TTCTCTGTTG
* * *
178704 TTGATATCTATGATGTGATTGGTTGTCATTTCTTTGTTGTTGATTACAGGTGATTTTGATATATG
1 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCTG
*
178769 TGATATGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGATT
66 TGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGATT
*
178834 TGTTGTCATTTCTCTGTTGTTGATTACAGGTGATA
131 TGTTGTCATTTATCTGTTGTTGATTACAGGTGATA
*
178869 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATATG
1 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCTG
178934 TGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGATT
66 TGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGATT
* *
178999 TGTTGTCATTTCTCTTTTGTTGATTACAGGTGATA
131 TGTTGTCATTTATCTGTTGTTGATTACAGGTGATA
179034 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCTG
1 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCTG
*
179099 TGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGAAATCTGTGATGTGATT
66 TGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGATT
*
179164 TGTTGTCATTTATCTGTTGTTGATTATAGGTGATA
131 TGTTGTCATTTATCTGTTGTTGATTACAGGTGATA
* * * * ** *
179199 TTGATATCTATGATGTGATTGTTTGTCATTTCTTTTTTGTTGATTACAAATGATATTGATATCTG
1 TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCTG
* * * * *
179264 TGATGTGATTG-TTTGTCATTTCTCTGTTGTTGATTACAAATGATATTGATATATGTGACGTGGT
66 TGATGTGATTGATTT-TCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGAT
* *
179328 TTATTGTCATTTATCTGGTGTT-ATATACAGGTGATA
130 TTGTTGTCATTTATCTGTTGTTGAT-TACAGGTGATA
* * ** *
179364 TCGATATCTGTGAT-TG-TCT--TT-TCATTTCTCTGTTGTTGATTGCAAATGATATTGATATCT
1 TTGATATCTGTGATGTGAT-TGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCT
* *
179424 GTGATGTGATTGATTTTCATTTCTCTGTTGCTT-CTTACAGGTGATATTGATATCTGTGATGTGA
65 GTGATGTGATTGATTTTCATTTCTCTGTTG-TTGGTTACAGATGATATTGATATCTGTGATGTGA
179488 TT
129 TT
179490 GGGTGTCACC
Statistics
Matches: 580, Mismatches: 36, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
161 89 0.15
162 7 0.01
163 1 0.00
164 8 0.01
165 475 0.82
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.49
Consensus pattern (165 bp):
TTGATATCTGTGATGTGATTGGTTGTCATTTCTCTGTTGTTGATTACAGGTGATTTTGATATCTG
TGATGTGATTGATTTTCATTTCTCTGTTGTTGGTTACAGATGATATTGATATCTGTGATGTGATT
TGTTGTCATTTATCTGTTGTTGATTACAGGTGATA
Found at i:179804 original size:15 final size:15
Alignment explanation
Indices: 179778--179818 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
179768 TTACTAGTAT
179778 TATATCAGATATATTA
1 TATAT-AGATATATTA
179794 TATATAGATATATTA
1 TATATAGATATATTA
179809 TATATAGATA
1 TATATAGATA
179819 ATCTCAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (15 bp):
TATATAGATATATTA
Found at i:181996 original size:19 final size:19
Alignment explanation
Indices: 181969--182005 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
181959 AAAGAATATT
*
181969 TTTTTTGTCTTAAAGACAC
1 TTTTCTGTCTTAAAGACAC
*
181988 TTTTCTGTCTTATAGACA
1 TTTTCTGTCTTAAAGACA
182006 TATTTTAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (19 bp):
TTTTCTGTCTTAAAGACAC
Found at i:201833 original size:16 final size:16
Alignment explanation
Indices: 201786--201836 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
201776 CTGACTGAAA
* *
201786 TATATATGTCACTAAA
1 TATATATGCCACTAAG
201802 TATATATGCCACTAAG
1 TATATATGCCACTAAG
201818 TATATATGCCACTAAG
1 TATATATGCCACTAAG
201834 TAT
1 TAT
201837 GCCACTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (16 bp):
TATATATGCCACTAAG
Found at i:202445 original size:12 final size:13
Alignment explanation
Indices: 202425--202453 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
202415 TCCCTGAATA
202425 AAAATTTGAATTT
1 AAAATTTGAATTT
202438 AAAA-TTGAATTT
1 AAAATTTGAATTT
202450 AAAA
1 AAAA
202454 AAAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
AAAATTTGAATTT
Found at i:210213 original size:2 final size:2
Alignment explanation
Indices: 210206--210248 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
210196 AAATTTCCCA
210206 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
210248 T
1 T
210249 TAAAGGTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:213685 original size:11 final size:11
Alignment explanation
Indices: 213669--213694 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
213659 CTATCATACT
213669 GATCATTTTAA
1 GATCATTTTAA
213680 GATCATTTTAA
1 GATCATTTTAA
213691 GATC
1 GATC
213695 TAACACTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (11 bp):
GATCATTTTAA
Found at i:213778 original size:1 final size:1
Alignment explanation
Indices: 213772--213799 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
213762 AGCATTGAGT
213772 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
213800 TTAGGAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:219615 original size:69 final size:69
Alignment explanation
Indices: 219504--219866 Score: 379
Period size: 69 Copynumber: 5.2 Consensus size: 69
219494 AGGTCACATC
*
219504 ACAGCTCGCTGAGGCGACAGCTCAAAACACTGAGCTGCTCAATAAACGAGAGGTATGTTTGTAGA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATAAACGAGAGGTATGTTTGTAGA
219569 CCTT
66 CCTT
**
219573 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATATAAACGAGAGGTATACTTGTA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTC-A-ATAAACGAGAGGTATGTTTGTA
219638 GACCTT
64 GACCTT
* * * *
219644 ACAGCTCGCTGAGTCGACAGCTCAAAACACAGAGCTGCTCAATAAATGAGAGGTTTGTTAGTAGA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATAAACGAGAGGTATGTTTGTAGA
*
219709 TCTT
66 CCTT
*** * * * * * * * * *
219713 ACAGCTTATTGAAGCAACAGCTCAAAACACTTGAGTTGATCAACAAAACAAGAGGTATGTTAGAA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACAC-AGAGCTGCTCAA-TAAACGAGAGGTATGTTTGTA
*
219778 GACCTC
64 GACCTT
* * * * * * ** *
219784 ACAGCTCACTGAGGC-AGCTGTTTAAAACACCA-AGCTGCACAACAAATTAGAGGTATTTTTGTA
1 ACAGCTCGCTGAGGCGA-CAGCTCAAAACA-CAGAGCTGCTCAATAAACGAGAGGTATGTTTGTA
219847 GACCTT
64 GACCTT
*
219853 AAAGCTCGCTGAGG
1 ACAGCTCGCTGAGG
219867 TAACACTTAG
Statistics
Matches: 243, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
69 117 0.48
70 19 0.08
71 106 0.44
72 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (69 bp):
ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATAAACGAGAGGTATGTTTGTAGA
CCTT
Found at i:219662 original size:71 final size:71
Alignment explanation
Indices: 219504--219687 Score: 318
Period size: 71 Copynumber: 2.6 Consensus size: 71
219494 AGGTCACATC
* **
219504 ACAGCTCGCTGAGGCGACAGCTCAAAACACTGAGCTGCTC-A-ATAAACGAGAGGTATGTTTGTA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATATAAACGAGAGGTATACTTGTA
219567 GACCTT
66 GACCTT
219573 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATATAAACGAGAGGTATACTTGTA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATATAAACGAGAGGTATACTTGTA
219638 GACCTT
66 GACCTT
*
219644 ACAGCTCGCTGAGTCGACAGCTCAAAACACAGAGCTGCTCAATA
1 ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATA
219688 AATGAGAGGT
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
69 39 0.36
70 1 0.01
71 69 0.63
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (71 bp):
ACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATATAAACGAGAGGTATACTTGTA
GACCTT
Found at i:219767 original size:140 final size:140
Alignment explanation
Indices: 219502--219864 Score: 383
Period size: 140 Copynumber: 2.6 Consensus size: 140
219492 TCAGGTCACA
* *
219502 TCACAGCTCGCTGAGGCGACAGCTCAAAACACTGAGCTGCTCAATAAACGAGAGGTATGTTTGTA
1 TCACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATAAACGAGAGGTATGTTAGTA
* * * * * *
219567 GACCTTACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATATAAACGAGAGGTATA
66 GACCTTACAGCTCACTGAAGCAACAGCTCAAAACACAGAGCTGATCAACATAAACAAGAGGTAT-
*
219632 CTT-GTAGACC
130 CTTAGAAGACC
* * * *
219642 TTACAGCTCGCTGAGTCGACAGCTCAAAACACAGAGCTGCTCAATAAATGAGAGGTTTGTTAGTA
1 TCACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATAAACGAGAGGTATGTTAGTA
* * * * *
219707 GATCTTACAGCTTATTGAAGCAACAGCTCAAAACACTTGAGTTGATCAACA-AAACAAGAGGTAT
66 GACCTTACAGCTCACTGAAGCAACAGCTCAAAACAC-AGAGCTGATCAACATAAACAAGAGGTAT
*
219771 GTTAGAAGACC
130 CTTAGAAGACC
* * * * * * ** * *
219782 TCACAGCTCACTGAGGC-AGCTGTTTAAAACACCA-AGCTGCACAACAAATTAGAGGTATTTTTG
1 TCACAGCTCGCTGAGGCGA-CAGCTCAAAACA-CAGAGCTGCTCAATAAACGAGAGGTATGTTAG
* *
219845 TAGACCTTAAAGCTCGCTGA
64 TAGACCTTACAGCTCACTGA
219865 GGTAACACTT
Statistics
Matches: 183, Mismatches: 36, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
139 3 0.02
140 168 0.92
141 12 0.07
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (140 bp):
TCACAGCTCGCTGAGGCGACAGCTCAAAACACAGAGCTGCTCAATAAACGAGAGGTATGTTAGTA
GACCTTACAGCTCACTGAAGCAACAGCTCAAAACACAGAGCTGATCAACATAAACAAGAGGTATC
TTAGAAGACC
Found at i:230035 original size:256 final size:256
Alignment explanation
Indices: 229563--230052 Score: 677
Period size: 256 Copynumber: 1.9 Consensus size: 256
229553 CAATGGGGGA
* * * *
229563 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTTTTTCTTAAACACTATTAGA
1 TCAAGTTTTACATAGGAATACATAGAGAAAATCTTAAAAAATCTTTTCTCTAAAACACTATTAGA
* ** *
229628 CCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTTAGGTAGTGTAGATTCAAGTTTGTTCAAATCA
66 CCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTTAGATAGTAAAGATTCAAATTTGTTCAAATCA
* ** **
229693 TAGTCCCTTGGGGTAGGATGGGGCCACAATGAGGGAATGGATTTTTACATAAGAATGTATAGAGA
131 TAGTCCCTGGGGGTAGGATGGGGCCACAATGAGGGAATCAAGGTTTACATAAGAA-GTATAGAGA
*
229758 AAATCTTTAAAAATCTTCTTCTCAAAAACTATTTGGCTAAAGCATCCTCAGATAGTGTAGAT
195 AAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCTAAAGCATCCTCAGATAGTGTAGAT
229820 TCAAGTTTTACATAGGAATACATAGAGAAAATCTTAAAAAATCTTCTTCTC-AAAAC-CTATTAG
1 TCAAGTTTTACATAGGAATACATAGAGAAAATCTTAAAAAATCTT-TTCTCTAAAACACTATTAG
* * *
229883 GCCAGAAAAGCTCAAATTTGAGTGGAATCATCCTTAGATAGTAAAGATTCAAATTTGTTCAAATC
65 ACCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTTAGATAGTAAAGATTCAAATTTGTTCAAATC
* * * * *
229948 ATGGTTCCTGGGGGTTAGGGTGGGGCCACAAT-AGGGGGATCAAGGTTTGCA-AAGGAA-TATAG
130 ATAGTCCCTGGGGG-TAGGATGGGGCCACAATGA-GGGAATCAAGGTTTACATAA-GAAGTATAG
230010 AGAAAATCTTTAAAAAAAT-TTCTTCTCAAAAACTATTAGGCTA
192 AGAAAATCTTT--AAAAATCTTCTTCTCAAAAACTATTAGGCTA
230053 GAAAAGCTCA
Statistics
Matches: 205, Mismatches: 22, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
255 16 0.08
256 102 0.50
257 83 0.40
258 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (256 bp):
TCAAGTTTTACATAGGAATACATAGAGAAAATCTTAAAAAATCTTTTCTCTAAAACACTATTAGA
CCAGAAAAGCTCAAATTAGAGTGGAAGCATCCTTAGATAGTAAAGATTCAAATTTGTTCAAATCA
TAGTCCCTGGGGGTAGGATGGGGCCACAATGAGGGAATCAAGGTTTACATAAGAAGTATAGAGAA
AATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCTAAAGCATCCTCAGATAGTGTAGAT
Found at i:230339 original size:165 final size:164
Alignment explanation
Indices: 229825--230385 Score: 727
Period size: 164 Copynumber: 3.4 Consensus size: 164
229815 TAGATTCAAG
* * * *
229825 TTTTACATAGGAATACATAGAGAAAATCTTAAAAAATCTTCTTCTCAAAACCTATTAGGCCAGAA
1 TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGTCAGAA
* * * * *
229890 AAGCTCAAATTTGAGTGGAATCATCCTTAGATAGTAAAGATTCAAATTTGTTCAAATCATGGTTC
66 AAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTATAGATTCAAATTTGTTCAAATCATAGTCC
* * * * *
229955 CTGGGGGTTAGGGTGGGGCCACAATAGGGGGATCAAG
131 CCGGGGG-TAGGGTGAGGCCACAGT--GGGGATGAAT
* * *
229992 GTTTGCAAAGG-A-ATATAGAGAAAATCTTTAAAAAAAT-TTCTTCTCAAAAACTATTAGG-CTA
1 TTTTACATAGGAATATATAGAGAAAATCTTT--AAAAATCTTCTTCTCAAAAACTATTAGGTC-A
** * * *
230053 GAAAAGCTCAAATTAAAGTGGAAGCATCCACAGATAGTGTAGATTCAAATTTGTTTAAATCATAG
63 GAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTATAGATTCAAATTTGTTCAAATCATAG
* *
230118 TCCCGGGGGGTAGGGTGAGGCCACAGTGGGGGTGAAT
128 TCCCCGGGGGTAGGGTGAGGCCACAGTGGGGATGAAT
* * *
230155 TTTTACATAGGATTATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGATCAGGA
1 TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGTCAGAA
*
230220 AAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTATAGATTCAAGTTTGTTCAAATCATAGTCC
66 AAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTATAGATTCAAATTTGTTCAAATCATAGTCC
** *
230285 CCATGGGTAGGGTGAGGCCACAGTGTTGGATGAAT
131 CCGGGGGTAGGGTGAGGCCACAGTG-GGGATGAAT
* *
230320 TTTTACATAGGAATATATAGAGAAAATATTTAAAAATCTTCTT-TTAAAAACTATTAGGTCAGAA
1 TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGTCAGAA
230384 AA
66 AA
230386 ACTTTTGTAG
Statistics
Matches: 342, Mismatches: 44, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
163 21 0.06
164 124 0.36
165 97 0.28
166 86 0.25
167 14 0.04
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (164 bp):
TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGTCAGAA
AAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTATAGATTCAAATTTGTTCAAATCATAGTCC
CCGGGGGTAGGGTGAGGCCACAGTGGGGATGAAT
Found at i:241182 original size:166 final size:165
Alignment explanation
Indices: 240569--241435 Score: 915
Period size: 168 Copynumber: 5.3 Consensus size: 165
240559 GGCATTTTTC
** * * *
240569 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTGTTACTTGTA-TGGAAGTATTCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCT-CAAATTG-AGTGGAAGCATCCTCAG
* * * * *
240633 ACAGTGTGGATTTAAATTTGTTCAAATCATGGTCCCCAGGGGTAGGGCGGGGCCACAATGGCGGG
64 ACAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* *
240698 ATGAATTTTTTTAAATAGGAATATATAGAGGAAATCTTT
129 ATGAA--TTTTTAAATGGGAATATATAGAGAAAATCTTT
* * ** * *
240737 AAAACTCTTGTTCTCAAAAGGTATTAGGCCAGAAAAGCTCACATTAGAGTGGAAGCATCCTCAGT
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-GAGTGGAAGCATCCTCAGA
* * *
240802 C--TGTAGATTCAAATTTGTTTAAATCATGGTCCCCGGGGGTAGGGCGGGGCCACGAT-GGGGGA
65 CAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
*
240864 TGAATTTTTAAATAGGAATATATAGAGAAAATCTTT
130 TGAATTTTTAAATGGGAATATATAGAGAAAATCTTT
* *
240900 AAAAATC-T-TT-TGAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAGGCATCCTCAG-
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCAGA
* * * * * * *
240961 TA-T-T-GATTTAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGTGTGGGGGCACAATGGAGGTA
65 CAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGA
* * * * * *
241023 TCAAGTTTTACATGGGAACATGTTGAGAAAATCTTT
130 TGAATTTTTAAATGGGAATATATAGAGAAAATCTTT
* * *
241059 AATAAAT-TTCTTCTCAAAAACTATT-GGACCAGACAAGCTTAAACTTGTGTGGAAGCATCCTCA
1 AA-AAATCTTCTTCTCAAAAACTATTAGG-CCAGAAAAGCTCAAA-TTGAGTGGAAGCATCCTCA
* * * * *
241122 GACAGTGTAGAATCAAATTTGTTCAAATTATAGTCCTCAGGGGTAGGGTGGGGCCACAATGGGGG
63 GACAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAT--GGG
* * *
241187 GGGGTGAATTTTTAAATGGAAATATATGGAGAAAATCTTT
126 GGGATGAATTTTTAAATGGGAATATATAGAGAAAATCTTT
* * * * *
241227 AAAAATCTTCTTCTTAAAAACTATTAGGCCAGGAAAGCTCAGATTGGAGT-CAAGGCATTCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-GAGTGGAA-GCATCCTCAG
* * * *
241291 ATAGTTTAGATTCAAATTTGTTCAAATCATGGTCTCTGGGGGTAGGGTGGGGCCACAATGGGGGG
64 ACAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
** * * *
241356 ATCTAGTTTTACATGGGAATATAAAGA-AAACATCTTT
129 ATGAATTTTTAAATGGGAATATATAGAGAAA-ATCTTT
*
241393 AAAAA---TCTTCTCAAAAAGTATTAGGCCAGAAAAGCTCAAATTG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTG
241436 GAGGGAAAAG
Statistics
Matches: 582, Mismatches: 96, Indels: 48
0.80 0.13 0.07
Matches are distributed among these distances:
158 44 0.08
159 36 0.06
160 49 0.08
161 8 0.01
162 44 0.08
163 71 0.12
164 1 0.00
165 13 0.02
166 128 0.22
167 11 0.02
168 175 0.30
169 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTGAGTGGAAGCATCCTCAGAC
AGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGAT
GAATTTTTAAATGGGAATATATAGAGAAAATCTTT
Found at i:255142 original size:2 final size:2
Alignment explanation
Indices: 255135--255206 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
255125 AAAGATAAAT
*
255135 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
255177 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
255207 CACTTGACAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:262935 original size:212 final size:212
Alignment explanation
Indices: 262568--262990 Score: 792
Period size: 212 Copynumber: 2.0 Consensus size: 212
262558 ACAGGGAGTA
*
262568 GCGTTGTTTGGTTCTGAGCAGGCGTAAAAAGCAACAACTTTGACGGCGGATATCTCGCTTATTAA
1 GCGTTGTTTGGTTCTGACCAGGCGTAAAAAGCAACAACTTTGACGGCGGATATCTCGCTTATTAA
* *
262633 GCTGTTAATAAAAATTTAGTTTTTTGTACTTGGTTATTATTTTTTAAAACGTAATTGAAACGGAT
66 GCCGTTAATAAAAATTTAGTTTTTTGTACTTGGTTATTATTTTTTAAAACGCAATTGAAACGGAT
*
262698 TTTAACTTTTAACATCATCTTTCACGCTTTCTCTGAGCAGAGCTGTGTTGAAAAAACATAGCATC
131 TTTAACTTTTAACATCATCTTTCACGCTTTCTCTGAGCAGAGCTGTGTTGAAAAAACAAAGCATC
262763 CGGTCGATCTGGAAGTG
196 CGGTCGATCTGGAAGTG
262780 GCGTTGTTTGGTTCTGACCAGGCGTAAAAAGCAACAACTTTGACGGCGGATATCTCGCTTATTAA
1 GCGTTGTTTGGTTCTGACCAGGCGTAAAAAGCAACAACTTTGACGGCGGATATCTCGCTTATTAA
262845 GCCGTTAATAAAAATTTAGTTTTTTGTACTTGGTTATTATTTTTTAAAACGCAATTGAAACGGAT
66 GCCGTTAATAAAAATTTAGTTTTTTGTACTTGGTTATTATTTTTTAAAACGCAATTGAAACGGAT
* *
262910 TTTAACTTTTAACATCATCTTTCACGCTTTCTCTGAGCAGAGCTGTGTTGCAAAGACAAAGCATC
131 TTTAACTTTTAACATCATCTTTCACGCTTTCTCTGAGCAGAGCTGTGTTGAAAAAACAAAGCATC
262975 CGGTCGATCTGGAAGT
196 CGGTCGATCTGGAAGT
262991 TTATAATAGC
Statistics
Matches: 205, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
212 205 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (212 bp):
GCGTTGTTTGGTTCTGACCAGGCGTAAAAAGCAACAACTTTGACGGCGGATATCTCGCTTATTAA
GCCGTTAATAAAAATTTAGTTTTTTGTACTTGGTTATTATTTTTTAAAACGCAATTGAAACGGAT
TTTAACTTTTAACATCATCTTTCACGCTTTCTCTGAGCAGAGCTGTGTTGAAAAAACAAAGCATC
CGGTCGATCTGGAAGTG
Found at i:271253 original size:12 final size:12
Alignment explanation
Indices: 271232--271265 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
271222 CACCTGTTGT
271232 CCGT-CGTCTGC
1 CCGTCCGTCTGC
271243 CCGTCCGTCTGC
1 CCGTCCGTCTGC
271255 CCGTCCGTCTG
1 CCGTCCGTCTG
271266 TAAACTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.00, C:0.47, G:0.26, T:0.26
Consensus pattern (12 bp):
CCGTCCGTCTGC
Found at i:288504 original size:5 final size:5
Alignment explanation
Indices: 288494--288519 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
288484 CTCTTAACTG
288494 GTTCC GTTCC GTTCC GTTCC GTTCC G
1 GTTCC GTTCC GTTCC GTTCC GTTCC G
288520 CAAAGTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.23, T:0.38
Consensus pattern (5 bp):
GTTCC
Found at i:294156 original size:17 final size:17
Alignment explanation
Indices: 294134--294167 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
294124 CAGTTCTTAT
*
294134 TCCAAAGAGTATTGGCC
1 TCCAAACAGTATTGGCC
294151 TCCAAACAGTATTGGCC
1 TCCAAACAGTATTGGCC
294168 CGTAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (17 bp):
TCCAAACAGTATTGGCC
Found at i:307226 original size:2 final size:2
Alignment explanation
Indices: 307184--307216 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
307174 TATATATATA
307184 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
307217 AACATGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:316092 original size:22 final size:24
Alignment explanation
Indices: 316049--316104 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
316039 AGTAGATGTA
316049 GTTTGTTTGGGGGTTTTTTTT-TGTT
1 GTTT-TTTGGGGGTTTTTTTTGT-TT
316074 GTTTTTTGGGGG-TTTTTTTGTTT
1 GTTTTTTGGGGGTTTTTTTTGTTT
*
316097 CTTTTTTG
1 GTTTTTTG
316105 CATAAACATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 16 0.55
24 9 0.31
25 4 0.14
ACGTcount: A:0.00, C:0.02, G:0.29, T:0.70
Consensus pattern (24 bp):
GTTTTTTGGGGGTTTTTTTTGTTT
Found at i:316101 original size:23 final size:24
Alignment explanation
Indices: 316054--316104 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
316044 ATGTAGTTTG
* *
316054 TTTGGGGGTTTTTTTTTGTTGTTT
1 TTTGGGGGTTTTTTTGTGTTCTTT
316078 TTTGGGGGTTTTTTTGT-TTCTTT
1 TTTGGGGGTTTTTTTGTGTTCTTT
316101 TTTG
1 TTTG
316105 CATAAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.00, C:0.02, G:0.27, T:0.71
Consensus pattern (24 bp):
TTTGGGGGTTTTTTTGTGTTCTTT
Found at i:316160 original size:13 final size:13
Alignment explanation
Indices: 316142--316167 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
316132 TTAAAAGAGG
316142 TTTAAATTTTTAT
1 TTTAAATTTTTAT
316155 TTTAAATTTTTAT
1 TTTAAATTTTTAT
316168 GGTCATTCTA
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTAAATTTTTAT
Found at i:317933 original size:12 final size:12
Alignment explanation
Indices: 317916--317955 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
317906 CGTTGTCCGT
317916 CGTCCGTCTGTC
1 CGTCCGTCTGTC
317928 CGTCCGTCTGTC
1 CGTCCGTCTGTC
**
317940 CGTTTGTCTGTC
1 CGTCCGTCTGTC
317952 CGTC
1 CGTC
317956 TGTAAACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:327533 original size:42 final size:42
Alignment explanation
Indices: 327474--327560 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
327464 AAATACTCTT
327474 CCGGTCAGGACCGTAGCAATAGACCGTGGCTATTTATAGCCA
1 CCGGTCAGGACCGTAGCAATAGACCGTGGCTATTTATAGCCA
327516 CCGGTCAGGACCGTAGCAATAGACCGTGGCTATTTATAGCCA
1 CCGGTCAGGACCGTAGCAATAGACCGTGGCTATTTATAGCCA
327558 CCG
1 CCG
327561 TCTAAAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (42 bp):
CCGGTCAGGACCGTAGCAATAGACCGTGGCTATTTATAGCCA
Found at i:330563 original size:7 final size:7
Alignment explanation
Indices: 330551--330617 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
330541 GAGAAGGATC
330551 ATTCGAG
1 ATTCGAG
330558 ATTCGAG
1 ATTCGAG
* *
330565 ATTCAAA
1 ATTCGAG
*
330572 ATACGAG
1 ATTCGAG
*
330579 ATTCGAA
1 ATTCGAG
*
330586 ATACGAG
1 ATTCGAG
*
330593 ATTCAAG
1 ATTCGAG
*
330600 ATTCGAA
1 ATTCGAG
330607 ATTCGAG
1 ATTCGAG
330614 ATTC
1 ATTC
330618 AATATCTAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:331139 original size:2 final size:2
Alignment explanation
Indices: 331132--331168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
331122 TTGCCGATAT
331132 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
331169 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:348675 original size:21 final size:21
Alignment explanation
Indices: 348651--348761 Score: 152
Period size: 21 Copynumber: 5.3 Consensus size: 21
348641 AGCCGTCGGT
*
348651 TGTTGGGTTTGAGTTGTCAGG
1 TGTTGGGTTTGAGCTGTCAGG
* *
348672 TGTTGGGTTTGAGCTGCCGGG
1 TGTTGGGTTTGAGCTGTCAGG
348693 TGTTGGGTTTGAGCTGTCAGG
1 TGTTGGGTTTGAGCTGTCAGG
* *
348714 TGTTGGGTTTGAGCTGCCGGG
1 TGTTGGGTTTGAGCTGTCAGG
*
348735 TGTTGGATTTGAGCTGTC-GG
1 TGTTGGGTTTGAGCTGTCAGG
348755 ATGTTGG
1 -TGTTGG
348762 ATTCGAAGTC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 2 0.03
21 78 0.98
ACGTcount: A:0.08, C:0.10, G:0.44, T:0.38
Consensus pattern (21 bp):
TGTTGGGTTTGAGCTGTCAGG
Found at i:348697 original size:42 final size:42
Alignment explanation
Indices: 348651--348761 Score: 188
Period size: 42 Copynumber: 2.6 Consensus size: 42
348641 AGCCGTCGGT
*
348651 TGTTGGGTTTGAGTTGTCAGGTGTTGGGTTTGAGCTGCCGGG
1 TGTTGGGTTTGAGCTGTCAGGTGTTGGGTTTGAGCTGCCGGG
348693 TGTTGGGTTTGAGCTGTCAGGTGTTGGGTTTGAGCTGCCGGG
1 TGTTGGGTTTGAGCTGTCAGGTGTTGGGTTTGAGCTGCCGGG
*
348735 TGTTGGATTTGAGCTGTC-GGATGTTGG
1 TGTTGGGTTTGAGCTGTCAGG-TGTTGG
348762 ATTCGAAGTC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
41 2 0.03
42 64 0.97
ACGTcount: A:0.08, C:0.10, G:0.44, T:0.38
Consensus pattern (42 bp):
TGTTGGGTTTGAGCTGTCAGGTGTTGGGTTTGAGCTGCCGGG
Found at i:348781 original size:63 final size:62
Alignment explanation
Indices: 348651--348781 Score: 138
Period size: 63 Copynumber: 2.1 Consensus size: 62
348641 AGCCGTCGGT
* * * * * * * *
348651 TGTTGGGTTTGAGTTGTCAGGTGTTGGGTTTGAGCTGCCGGGTGTTGGGTTTGAGCTGTCAGG
1 TGTTGGGTTTGAGCTGCCAGGTGTTGGATTTGAGCTGCCGGATGTTGGATTCGA-CAGTCAGC
* *
348714 TGTTGGGTTTGAGCTGCCGGGTGTTGGATTTGAGCTGTCGGATGTTGGATTCGA-AGTCATTGC
1 TGTTGGGTTTGAGCTGCCAGGTGTTGGATTTGAGCTGCCGGATGTTGGATTCGACAGTCA--GC
348777 TGTTG
1 TGTTG
348782 TCGTGGTACT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
61 4 0.07
63 52 0.93
ACGTcount: A:0.10, C:0.11, G:0.41, T:0.38
Consensus pattern (62 bp):
TGTTGGGTTTGAGCTGCCAGGTGTTGGATTTGAGCTGCCGGATGTTGGATTCGACAGTCAGC
Found at i:350702 original size:21 final size:21
Alignment explanation
Indices: 350673--350736 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
350663 TTTTTCTATC
350673 AAATATGTTGACATGCAACTT
1 AAATATGTTGACATGCAACTT
** * * * **
350694 AGTTATGTTAATATGCGAGAT
1 AAATATGTTGACATGCAACTT
350715 AAATATGTTGACATGCAACTT
1 AAATATGTTGACATGCAACTT
350736 A
1 A
350737 TAAGTTGTAT
Statistics
Matches: 29, Mismatches: 14, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (21 bp):
AAATATGTTGACATGCAACTT
Found at i:350762 original size:21 final size:21
Alignment explanation
Indices: 350736--350894 Score: 156
Period size: 21 Copynumber: 7.6 Consensus size: 21
350726 CATGCAACTT
*
350736 ATAAGTTGTATGTCAACATAA
1 ATAAGTTGCATGTCAACATAA
*
350757 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
* * *
350778 ATATGTTGCGTGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** * *
350799 TTATCTTGCATGTTAACATGA
1 ATAAGTTGCATGTCAACATAA
* * *
350820 CTAAGTTGCATGTCGACATAC
1 ATAAGTTGCATGTCAACATAA
*
350841 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
* * *
350862 AGAAGTTGCACGTTAACATAA
1 ATAAGTTGCATGTCAACATAA
*
350883 AGAAGTTGCATG
1 ATAAGTTGCATG
350895 CTGACATCAA
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 112 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (21 bp):
ATAAGTTGCATGTCAACATAA
Found at i:350871 original size:63 final size:63
Alignment explanation
Indices: 350738--350894 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 63
350728 TGCAACTTAT
* * * * ***
350738 AAGTTGTATGTCAACATAAATAAGTTGCATGTCGACATAAATATGTTGCGTGTCAACATATTT
1 AAGTTGCATGTTAACATAAATAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAAG
** * * * *
350801 ATCTTGCATGTTAACATGACTAAGTTGCATGTCGACATACATAAGTTGCATGTCGACATAAAG
1 AAGTTGCATGTTAACATAAATAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAAG
* *
350864 AAGTTGCACGTTAACATAAAGAAGTTGCATG
1 AAGTTGCATGTTAACATAAATAAGTTGCATG
350895 CTGACATCAA
Statistics
Matches: 75, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (63 bp):
AAGTTGCATGTTAACATAAATAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAAG
Found at i:351033 original size:21 final size:21
Alignment explanation
Indices: 350985--351064 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 21
350975 ATTGCAGTTT
*
350985 TCTTGCATGTCAACAT-AGTA
1 TCTTGCATGTCAACATAACTA
* **
351005 TGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAACTA
**
351026 TCTTGCATGTCAACATATTTA
1 TCTTGCATGTCAACATAACTA
*
351047 TCTTGCATGTCGACATAA
1 TCTTGCATGTCAACATAA
351065 TAAATAGAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 13 0.27
21 35 0.73
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (21 bp):
TCTTGCATGTCAACATAACTA
Found at i:351042 original size:41 final size:42
Alignment explanation
Indices: 350985--351064 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
350975 ATTGCAGTTT
* *
350985 TCTTGCATGTCAACATA-GTATGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATATGTATCTTGCATGTCGACATAACTA
*
351026 TCTTGCATGTCAACATATTTATCTTGCATGTCGACATAA
1 TCTTGCATGTCAACATATGTATCTTGCATGTCGACATAA
351065 TAAATAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 17 0.49
42 18 0.51
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (42 bp):
TCTTGCATGTCAACATATGTATCTTGCATGTCGACATAACTA
Found at i:354164 original size:10 final size:10
Alignment explanation
Indices: 354149--354179 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
354139 ACATTTAATG
354149 TCTCAGTTAA
1 TCTCAGTTAA
*
354159 TCTCAGCTAA
1 TCTCAGTTAA
354169 TCTCAGTTAA
1 TCTCAGTTAA
354179 T
1 T
354180 TCTTTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (10 bp):
TCTCAGTTAA
Found at i:354303 original size:21 final size:21
Alignment explanation
Indices: 354266--354306 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
354256 GGTGGTTGGG
*
354266 GGTGGTTGTGTAGTGGTAGTC
1 GGTGGTTGGGTAGTGGTAGTC
354287 GGTGGTTGGGT-GATGGTAGT
1 GGTGGTTGGGTAG-TGGTAGT
354307 TGAGGGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.10, C:0.02, G:0.51, T:0.37
Consensus pattern (21 bp):
GGTGGTTGGGTAGTGGTAGTC
Found at i:355614 original size:2 final size:2
Alignment explanation
Indices: 355601--355645 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
355591 GATTTCAATA
* * *
355601 AG AG AT AG AG AG AG AA AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
355643 AG A
1 AG A
355646 TATTTTACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (2 bp):
AG
Found at i:362023 original size:15 final size:17
Alignment explanation
Indices: 362002--362044 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
361992 CAACGTCCCA
362002 AGCGAAACGTCTTT-GG
1 AGCGAAACGTCTTTAGG
*
362018 -GCGAAATGTCTTTAGG
1 AGCGAAACGTCTTTAGG
362034 AGCGAAACGTC
1 AGCGAAACGTC
362045 CCGCATTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 2 0.09
17 9 0.39
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (17 bp):
AGCGAAACGTCTTTAGG
Found at i:377383 original size:16 final size:16
Alignment explanation
Indices: 377362--377392 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
377352 AAGAAATTAC
*
377362 TTCGTTATATCCGTAA
1 TTCGTTATAACCGTAA
377378 TTCGTTATAACCGTA
1 TTCGTTATAACCGTA
377393 TAAGAAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TTCGTTATAACCGTAA
Found at i:394370 original size:21 final size:22
Alignment explanation
Indices: 394324--394370 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
394314 ATTTTTCGAG
*
394324 TGAAAAATGATAATTTTCGACA
1 TGAAAAATGATAATTGTCGACA
394346 -GAAAAATGATAATGTGT-GA-A
1 TGAAAAATGATAAT-TGTCGACA
394366 TGAAA
1 TGAAA
394371 TTATCTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 1 0.05
21 19 0.86
22 2 0.09
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (22 bp):
TGAAAAATGATAATTGTCGACA
Found at i:397716 original size:20 final size:21
Alignment explanation
Indices: 397691--397733 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
397681 GTTAAAGTTA
*
397691 TTATCTTGCATGTC-ACATAT
1 TTATCTAGCATGTCGACATAT
397711 TTATCTAGCATGTCGACATAT
1 TTATCTAGCATGTCGACATAT
397732 TT
1 TT
397734 GATTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (21 bp):
TTATCTAGCATGTCGACATAT
Found at i:403667 original size:3 final size:3
Alignment explanation
Indices: 403659--403703 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
403649 AAATTTGGAT
* *
403659 GAA GAA GAA TAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
403704 AGTCGACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:404666 original size:15 final size:15
Alignment explanation
Indices: 404646--404677 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
404636 GAAATGTATT
404646 TAATTTAAGTACATG
1 TAATTTAAGTACATG
*
404661 TAATTTGAGTACATG
1 TAATTTAAGTACATG
404676 TA
1 TA
404678 TGTCTAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (15 bp):
TAATTTAAGTACATG
Found at i:416704 original size:166 final size:164
Alignment explanation
Indices: 416408--416730 Score: 556
Period size: 166 Copynumber: 2.0 Consensus size: 164
416398 CTCTTAAATA
* * *
416408 TTTTATTCAATGTAGTTTATTTAGCATTGTAAAATATGAATATACAAGTAGAAATCAAATGTGAT
1 TTTTATTCAATGCAGTTTATTTAGCATTGTAAAATATGAATAAACAAGTAGAAATCAAATGCGAT
* * *
416473 GCAGAATTTTCAGAATGAAGGTGATTCAAATTTGTTACCTCAAAACAGAGGAACGAACCTCTTTA
66 GCAGAATTTTCAGAATAAAGGTGATTCAAATTGGCTACCTCAAAACAGAGGAACGAACCTCTTTA
416538 AAGCTCCAAGTACAAATACATCGATATGNTTCAAT
131 AAGCTCCAAGTACAAATACATCGATATG-TTCAAT
* *
416573 TTTTATTCAATGCAGTTTTTTTAAGCATTGTAAAATATGAATAAACAAGTTGAAATCAAATGCGA
1 TTTTATTCAATGCAGTTTATTT-AGCATTGTAAAATATGAATAAACAAGTAGAAATCAAATGCGA
416638 TGCAGAATTTTCAGAATAAAGGTGATTCAAATTGGCTACCTCAAAACAGAGGAACGAACCTCTTT
65 TGCAGAATTTTCAGAATAAAGGTGATTCAAATTGGCTACCTCAAAACAGAGGAACGAACCTCTTT
416703 AAAGCTCCAAGTACAAATACATCGATAT
130 AAAGCTCCAAGTACAAATACATCGATAT
416731 TAAATGATAT
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
165 20 0.13
166 129 0.87
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (164 bp):
TTTTATTCAATGCAGTTTATTTAGCATTGTAAAATATGAATAAACAAGTAGAAATCAAATGCGAT
GCAGAATTTTCAGAATAAAGGTGATTCAAATTGGCTACCTCAAAACAGAGGAACGAACCTCTTTA
AAGCTCCAAGTACAAATACATCGATATGTTCAAT
Found at i:417209 original size:205 final size:204
Alignment explanation
Indices: 416856--417266 Score: 813
Period size: 205 Copynumber: 2.0 Consensus size: 204
416846 CTCGGNCCCC
416856 CAAAAAAAAATACCAGAAGTTTTAAAATAAAACAAATGATCAAGATCTTTTATTATATCCCTTTT
1 CAAAAAAAAATACCAGAAGTTTTAAAATAAAACAAATGATCAAGATCTTTTATTATATCCCTTTT
416921 TCCTTAGCCTGCTGTTTTCTTGAACTGTTATATATTAGTTCCTTTAATAAGTGTTATGATTCATC
66 TCCTTAGCCTGCTGTTTTCTTGAACTGTTATATATTAGTTCCTTTAATAAGTGTTATGATTCATC
416986 TATTACTCGTTACTTTTGGGATTACAGATTGAAAATTTGAAGGTTTTATGTGGTTAAAAATACCT
131 TATTACTCGTTACTTTTGGGATTACAGATTGAAAATTTGAAGGTTTTATGTGGTTAAAAATACCT
417051 TCTGGCACA
196 TCTGGCACA
417060 CNAAAAAAAAATACCAGAAGTTTTAAAATAAAACAAATGATCAAGATCTTTTATTATATCCCTTT
1 C-AAAAAAAAATACCAGAAGTTTTAAAATAAAACAAATGATCAAGATCTTTTATTATATCCCTTT
417125 TTCCTTAGCCTGCTGTTTTCTTGAACTGTTATATATTAGTTCCTTTAATAAGTGTTATGATTCAT
65 TTCCTTAGCCTGCTGTTTTCTTGAACTGTTATATATTAGTTCCTTTAATAAGTGTTATGATTCAT
417190 CTATTACTCGTTACTTTTGGGATTACAGATTGAAAATTTGAAGGTTTTATGTGGTTAAAAATACC
130 CTATTACTCGTTACTTTTGGGATTACAGATTGAAAATTTGAAGGTTTTATGTGGTTAAAAATACC
417255 TTCTGGCACA
195 TTCTGGCACA
417265 CA
1 CA
417267 GTGTAATCCC
Statistics
Matches: 206, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
204 2 0.01
205 204 0.99
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (204 bp):
CAAAAAAAAATACCAGAAGTTTTAAAATAAAACAAATGATCAAGATCTTTTATTATATCCCTTTT
TCCTTAGCCTGCTGTTTTCTTGAACTGTTATATATTAGTTCCTTTAATAAGTGTTATGATTCATC
TATTACTCGTTACTTTTGGGATTACAGATTGAAAATTTGAAGGTTTTATGTGGTTAAAAATACCT
TCTGGCACA
Found at i:417957 original size:27 final size:26
Alignment explanation
Indices: 417917--417969 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
417907 TCGAGAAACA
*
417917 CTATTAAAAGGTATTATTTTCAATGT
1 CTATTAAAAGGTATTAGTTTCAATGT
417943 CTATTAAAAAGGTATTAGTTTCAATGT
1 CTATT-AAAAGGTATTAGTTTCAATGT
417970 GTGATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (26 bp):
CTATTAAAAGGTATTAGTTTCAATGT
Found at i:422835 original size:22 final size:22
Alignment explanation
Indices: 422810--422862 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
422800 ACCATTCACA
* *
422810 TTGATATGACATTATTTTTATG
1 TTGATATGACATAATGTTTATG
*
422832 TTGATATGACGTAATGTTTATG
1 TTGATATGACATAATGTTTATG
422854 TTGATATGA
1 TTGATATGA
422863 TGTTGTCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (22 bp):
TTGATATGACATAATGTTTATG
Found at i:423797 original size:2 final size:2
Alignment explanation
Indices: 423790--423819 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
423780 CAAAGCAAAA
*
423790 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
423820 CACATGACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:433334 original size:2 final size:2
Alignment explanation
Indices: 433327--433354 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
433317 ACCATCAAAA
433327 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
433355 GAGAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:434153 original size:2 final size:2
Alignment explanation
Indices: 434148--434188 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
434138 CCCTGCACAC
*
434148 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
434189 AGGACACGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:438188 original size:3 final size:3
Alignment explanation
Indices: 438182--438219 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
438172 CTAGGCCTAT
438182 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
438220 TTAATATTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:446232 original size:15 final size:15
Alignment explanation
Indices: 446206--446245 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
446196 AATTAACCCC
446206 AATATATAATACATGT
1 AATAT-TAATACATGT
*
446222 AATATTAATACATTT
1 AATATTAATACATGT
446237 AAT-TTAATA
1 AATATTAATA
446246 AATTAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 12 0.52
16 5 0.22
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
AATATTAATACATGT
Found at i:447872 original size:24 final size:25
Alignment explanation
Indices: 447843--447904 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
447833 CCTTACCCAA
*
447843 AGACACTCTAGAAAACCTT-CAAAG
1 AGACACTCTAGAAAACCTTACAAAC
**
447867 AGACACT-TGAGAAAATGTTACAAAC
1 AGACACTCT-AGAAAACCTTACAAAC
*
447892 AGAAACTCTAGAA
1 AGACACTCTAGAA
447905 TAATCTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 15 0.48
25 14 0.45
26 1 0.03
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (25 bp):
AGACACTCTAGAAAACCTTACAAAC
Found at i:447937 original size:25 final size:26
Alignment explanation
Indices: 447892--447941 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
447882 TGTTACAAAC
447892 AGAAACTCTAGAATAATCTTATCCAT
1 AGAAACTCTAGAATAATCTTATCCAT
447918 AGAAACTCTA-AATAATCTTATCCA
1 AGAAACTCTAGAATAATCTTATCCA
447942 GCCATATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (26 bp):
AGAAACTCTAGAATAATCTTATCCAT
Found at i:458751 original size:171 final size:170
Alignment explanation
Indices: 458465--458916 Score: 814
Period size: 171 Copynumber: 2.6 Consensus size: 170
458455 TCACACTTTT
*
458465 TTGTAAGCGCTCTCATGCCTACAAATTTTGATGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAA-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
458530 CCACTATTACCTTGGTCAAGTTCGAAAATCAGCTTTGGTCGATACTTTTTGTTGGAGTTATGGGA
65 CCACTAATACCTTGGTCAAGTTCGAAAATCAGC-TTGGTCGATACTTTTTGTTGGAGTTATGGGA
458595 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
129 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
458637 TTGTAAGCGCTCTCATGCCTACAAATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATAC
1 TTGTAAGCGCTCTCATGCCTACAAATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATAC
*
458702 CACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGAC
66 CACTAATACCTTGGTCAAGTTCGAAAATCAGC-TTGGTCGATACTTTTTGTTGGAGTTATGGGAC
458767 TTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
130 TTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
458808 TTGTAAGCGCTCTCATGCCTACAAAATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTAC-AAATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
**
458873 CCACTAATACCTTGGTCAAGTTCCTAAATCAGTCTTGGTCGATA
65 CCACTAATACCTTGGTCAAGTTCGAAAATCAG-CTTGGTCGATA
458917 GACTCGATAC
Statistics
Matches: 271, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
171 164 0.61
172 106 0.39
173 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (170 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATAC
CACTAATACCTTGGTCAAGTTCGAAAATCAGCTTGGTCGATACTTTTTGTTGGAGTTATGGGACT
TTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:468506 original size:38 final size:38
Alignment explanation
Indices: 468463--468539 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
468453 AGTATAATAA
468463 TATTATACTATAGGGTAAATTTTTTTCTCAGAAACAAG
1 TATTATACTATAGGGTAAATTTTTTTCTCAGAAACAAG
* *
468501 TATTATACTATAGGGTAATTTTTTTTCTCGGAAACAAG
1 TATTATACTATAGGGTAAATTTTTTTCTCAGAAACAAG
468539 T
1 T
468540 GCCTGTGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (38 bp):
TATTATACTATAGGGTAAATTTTTTTCTCAGAAACAAG
Found at i:475744 original size:23 final size:23
Alignment explanation
Indices: 475479--475737 Score: 394
Period size: 23 Copynumber: 11.3 Consensus size: 23
475469 GAGGACTTGG
* *
475479 GTAGTAAGTCCAGGATAACTGGA
1 GTAGTATGTCAAGGATAACTGGA
475502 GTAGTATGTCAAGGATAACTGGA
1 GTAGTATGTCAAGGATAACTGGA
475525 GTAGTATGTCAAGGATAACTGGA
1 GTAGTATGTCAAGGATAACTGGA
*
475548 GTAGTATGTCAAGGATATCTGGA
1 GTAGTATGTCAAGGATAACTGGA
* *
475571 GTAGTGTGTCAGGGATAACTGGA
1 GTAGTATGTCAAGGATAACTGGA
*
475594 GTAGTATGTCAAGGATAACTGCA
1 GTAGTATGTCAAGGATAACTGGA
475617 GTAGTATGTCAAGGATAACTGGA
1 GTAGTATGTCAAGGATAACTGGA
*
475640 GTAGTATGTCAAGGATAACTGCA
1 GTAGTATGTCAAGGATAACTGGA
* *
475663 GTAGTGTGGT-AAGAATAACTGGA
1 GTAGTAT-GTCAAGGATAACTGGA
* *
475686 GTAGTATTTCAAGGATAACTGCA
1 GTAGTATGTCAAGGATAACTGGA
*
475709 GTAGTATGTCAAGGATAACTGAA
1 GTAGTATGTCAAGGATAACTGGA
475732 GTAGTA
1 GTAGTA
475738 ACTCAAGAAG
Statistics
Matches: 214, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
22 1 0.00
23 211 0.99
24 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.27
Consensus pattern (23 bp):
GTAGTATGTCAAGGATAACTGGA
Found at i:475746 original size:69 final size:69
Alignment explanation
Indices: 475479--475781 Score: 392
Period size: 69 Copynumber: 4.4 Consensus size: 69
475469 GAGGACTTGG
* * *
475479 GTAGTAAGTCCAGGATAACTGGAGTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAAC
1 GTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGAATAAC
475544 TGGA
66 TGGA
* * * *
475548 GTAGTATGTCAAGGATATCTGGAGTAGTGTGTCAGGGATAACTGGAGTAGTATGTCAAGGATAAC
1 GTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGAATAAC
*
475613 TGCA
66 TGGA
* *
475617 GTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAACTGCAGTAGTGTGGT-AAGAATAA
1 GTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAACTGGAGTAGTAT-GTCAAGAATAA
475681 CTGGA
65 CTGGA
* * * ** **
475686 GTAGTATTTCAAGGATAACTGCAGTAGTATGTCAAGGATAACTGAAGTAGTAACTCAAGAAGCAC
1 GTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGAATAAC
*
475751 TTGA
66 TGGA
* * * *
475755 CTAGTACGTCAAAGATAACTTGAGTAG
1 GTAGTATGTCAAGGATAACTGGAGTAG
475782 CAAGTCGAGG
Statistics
Matches: 204, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
68 1 0.00
69 201 0.99
70 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (69 bp):
GTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGGATAACTGGAGTAGTATGTCAAGAATAAC
TGGA
Found at i:487525 original size:21 final size:20
Alignment explanation
Indices: 487458--487536 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
487448 GCGCCCCATG
*
487458 CACGAGCGCCCCAAATTTTTT
1 CACGAGCGCCCCAAA-TGTTT
*** *
487479 TTGGAGCGCCCCAATTACGTTT
1 CACGAGCGCCCCAA--ATGTTT
487501 CACGAGCGCCCCAAATGTATT
1 CACGAGCGCCCCAAATGT-TT
487522 CACGAGCGCCCCAAA
1 CACGAGCGCCCCAAA
487537 GTAAAATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.07
21 28 0.61
22 14 0.30
23 1 0.02
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (20 bp):
CACGAGCGCCCCAAATGTTT
Found at i:487799 original size:142 final size:142
Alignment explanation
Indices: 487544--487916 Score: 615
Period size: 142 Copynumber: 2.6 Consensus size: 142
487534 AAAGTAAAAT
* * *
487544 TATCATTATACCTTACTTCTTGGAA-AATTTGCACGAGCGCCCC-AAATTGGATTTGCCAATATT
1 TATCATTACACCTTACGTCTT-GAATAATTTGCACGAGCGCCCCAAAATTGGATTTTCCAATATT
*
487607 GTACTAAAATCGGGATCGTTTTCACGAGCGCCCCAAAATGATTTTCCTGATTATGTCTATCTGCA
65 GTACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAAATGATTTTCCTGATTATGTCTATCTGCA
* *
487672 TAGAATCTTTTTG
130 TAGAAACTTGTTG
* *
487685 TATCATTACACATTACGTCTTGAATAATTTGCCCGAGCGCCCCAAAATTGGATTTTCCAATATTG
1 TATCATTACACCTTACGTCTTGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTCCAATATTG
* *
487750 TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAAATGATTTTCCTGATTATGTCTTTCTGCTT
66 TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAAATGATTTTCCTGATTATGTCTATCTGCAT
487815 AGAAACTTGTTG
131 AGAAACTTGTTG
*
487827 TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTCCAATAATT
1 TATCATTACACCTTACGTCTTGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTCCAAT-ATT
487892 GTACTAAAATTGGGATCGTTTTCAC
65 GTACTAAAATTGGGATCGTTTTCAC
487917 CCCCCCCCCA
Statistics
Matches: 216, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
140 3 0.01
141 35 0.16
142 150 0.69
143 28 0.13
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (142 bp):
TATCATTACACCTTACGTCTTGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTCCAATATTG
TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAAATGATTTTCCTGATTATGTCTATCTGCAT
AGAAACTTGTTG
Found at i:488243 original size:64 final size:64
Alignment explanation
Indices: 488142--488261 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
488132 TCATCATGAA
488142 AAAAAAACATTTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGATCCAT
1 AAAAAAACATTTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGATCCAT
*
488206 AAAAAAACATTTGGGGCGCTCGTGACATACACGTGAAAAAAATTGATCATAAAAAA
1 AAAAAAACATTTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAA
488262 CAACATTTGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (64 bp):
AAAAAAACATTTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGATCCAT
Found at i:488246 original size:50 final size:52
Alignment explanation
Indices: 488192--488289 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
488182 AATTAATCAT
488192 AAAAAA-GGATCCAT-AAAAA-AACATTTGGGGCGCTCGTGACATACACGTGA
1 AAAAAATGGAT-CATAAAAAACAACATTTGGGGCGCTCGTGACATACACGTGA
*
488242 AAAAAATTGATCATAAAAAACAACATTTGGGGCGCTCGTGACATACAC
1 AAAAAATGGATCATAAAAAACAACATTTGGGGCGCTCGTGACATACAC
488290 TTGGGGCGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 9 0.20
51 8 0.18
52 27 0.61
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (52 bp):
AAAAAATGGATCATAAAAAACAACATTTGGGGCGCTCGTGACATACACGTGA
Found at i:491442 original size:140 final size:141
Alignment explanation
Indices: 491189--491469 Score: 467
Period size: 140 Copynumber: 2.0 Consensus size: 141
491179 TAAGAACACC
*
491189 CTTCCTATTAAAAGAAAGTTTTATAAATAAAAAGTTTTTACAAGTTTAATGGAAAAGGCATCTAA
1 CTTCCTATTAAAAGAAAGTTTTATAAATAAAAAGTTTATACAAGTTTAATGGAAAAGGCATCTAA
* * *
491254 AAAATCCCCTATCCGCTTCCGGATAAGACATTTTGCATCTTTGTGGTTTTAACAAGTGCATATAA
66 AAAATCCCCTATCCCCTTCCGGATAAGACATTTTGCATCTTTGCGGTTTAAACAAGTGCATATAA
491319 GTTTTA-TTTT
131 GTTTTACTTTT
* *
491329 CTTCCTATGT-AAAGAAAGTTTTATAAATAAAAGGTTTATACAATTTTAATGGAAAAGGCATCTA
1 CTTCCTAT-TAAAAGAAAGTTTTATAAATAAAAAGTTTATACAAGTTTAATGGAAAAGGCATCTA
* *
491393 AAAAATCCCCTATCCCCTTCCGGATAAGACATTTTGCATCTTTGCGGTTTAAACAAGTGCATGTG
65 AAAAATCCCCTATCCCCTTCCGGATAAGACATTTTGCATCTTTGCGGTTTAAACAAGTGCATATA
491458 AGTTTTACTTTT
130 AGTTTTACTTTT
491470 TCCCCTATCT
Statistics
Matches: 131, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
140 126 0.96
141 5 0.04
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (141 bp):
CTTCCTATTAAAAGAAAGTTTTATAAATAAAAAGTTTATACAAGTTTAATGGAAAAGGCATCTAA
AAAATCCCCTATCCCCTTCCGGATAAGACATTTTGCATCTTTGCGGTTTAAACAAGTGCATATAA
GTTTTACTTTT
Found at i:507769 original size:2 final size:2
Alignment explanation
Indices: 507764--507801 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
507754 GCCCCCCCTC
507764 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
507802 GACACACACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:519891 original size:2 final size:2
Alignment explanation
Indices: 519886--519931 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
519876 TTTTTTATTA
519886 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
519928 TG TG
1 TG TG
519932 GGAGGGGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:520525 original size:15 final size:14
Alignment explanation
Indices: 520492--520555 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
520482 GTGTTAAATG
* *
520492 TTTTGTTTTGCTTTG
1 TTTTG-TTTGTTTTT
520507 TTTTGTTTGTTTTAT
1 TTTTGTTTGTTTT-T
520522 TTTTGCTTTTGTTTTTT
1 TTTTG--TTTG-TTTTT
*
520539 TTTTTTTTGTTTTT
1 TTTTGTTTGTTTTT
520553 TTT
1 TTT
520556 GGGGGAGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 15 0.36
15 14 0.33
17 9 0.21
18 4 0.10
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (14 bp):
TTTTGTTTGTTTTT
Found at i:520531 original size:6 final size:5
Alignment explanation
Indices: 520490--520556 Score: 66
Period size: 5 Copynumber: 13.4 Consensus size: 5
520480 AAGTGTTAAA
* * *
520490 TGTTT TGTTT TGCTT TGTTT TG-TT TGTTT TATTTT TGCTTT TGTTT TTTTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T-GTTT TG-TTT TGTTT TGTTT
*
520541 TTTTT TGTTT T-TTT TG
1 TGTTT TGTTT TGTTT TG
520557 GGGGAGGGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
4 8 0.15
5 35 0.67
6 9 0.17
ACGTcount: A:0.01, C:0.03, G:0.15, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:520532 original size:36 final size:31
Alignment explanation
Indices: 520492--520555 Score: 83
Period size: 36 Copynumber: 1.9 Consensus size: 31
520482 GTGTTAAATG
520492 TTTTGTTTTGCTTTGTTTTGTTTGTTTTATTTTTGC
1 TTTTGTTTT--TTT-TTTT-TTTGTTTT-TTTTTGC
520528 TTTTGTTTTTTTTTTTTTTGTTTTTTTT
1 TTTTGTTTTTTTTTTTTTTGTTTTTTTT
520556 GGGGGAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 4 0.14
32 8 0.29
33 4 0.14
34 3 0.11
36 9 0.32
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (31 bp):
TTTTGTTTTTTTTTTTTTTGTTTTTTTTTGC
Found at i:520533 original size:21 final size:20
Alignment explanation
Indices: 520503--520556 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
520493 TTTGTTTTGC
520503 TTTGTTTTGTTTGTTTTATT
1 TTTGTTTTGTTTGTTTTATT
* *
520523 TTTGCTTTTGTTTTTTTTTTT
1 TTTG-TTTTGTTTGTTTTATT
*
520544 TTTGTTTTTTTTG
1 TTTGTTTTGTTTG
520557 GGGGAGGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (20 bp):
TTTGTTTTGTTTGTTTTATT
Found at i:520545 original size:26 final size:25
Alignment explanation
Indices: 520497--520545 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
520487 AAATGTTTTG
520497 TTTTGCTTTGTTTTGTTTGTTTTAT
1 TTTTGCTTTGTTTTGTTTGTTTTAT
* *
520522 TTTTGCTTTTGTTTTTTTTTTTTT
1 TTTTGC-TTTGTTTTGTTTGTTTT
520546 TGTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (25 bp):
TTTTGCTTTGTTTTGTTTGTTTTAT
Found at i:522672 original size:29 final size:29
Alignment explanation
Indices: 522621--522688 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
522611 ATGCATGGTA
*
522621 TACTTGTAT-TTTGTCGTGTAGTACGGTG
1 TACTTGTATATTTGTCGTGTAGTACGGAG
522649 TACTTGTATATTT-TCCGTGTAGTACGGAG
1 TACTTGTATATTTGT-CGTGTAGTACGGAG
*
522678 TATTTGTATAT
1 TACTTGTATAT
522689 CGTTTTGACG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.28
29 26 0.72
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (29 bp):
TACTTGTATATTTGTCGTGTAGTACGGAG
Found at i:526153 original size:2 final size:2
Alignment explanation
Indices: 526146--526188 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
526136 CCTATTACAC
526146 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
526188 A
1 A
526189 CTTAAGAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:528259 original size:2 final size:2
Alignment explanation
Indices: 528252--528292 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
528242 TTAGAGTGCC
528252 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
528293 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:537286 original size:15 final size:16
Alignment explanation
Indices: 537256--537291 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
537246 TCACCGAGAA
537256 GAGACATCACCCTTAT
1 GAGACATCACCCTTAT
*
537272 GAGACTTCA-CCTTAT
1 GAGACATCACCCTTAT
537287 GAGAC
1 GAGAC
537292 CACCTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (16 bp):
GAGACATCACCCTTAT
Found at i:537297 original size:13 final size:14
Alignment explanation
Indices: 537256--537297 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
537246 TCACCGAGAA
537256 GAGACATCACCCTTAT
1 GAGAC-TCA-CCTTAT
537272 GAGACTTCACCTTAT
1 GAGAC-TCACCTTAT
537287 GAGAC-CACCTT
1 GAGACTCACCTT
537298 TATCATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
15 11 0.44
16 8 0.32
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (14 bp):
GAGACTCACCTTAT
Found at i:537413 original size:4 final size:4
Alignment explanation
Indices: 537404--537446 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
537394 GACTTATGGC
537404 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
537447 ATACAAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:538958 original size:15 final size:15
Alignment explanation
Indices: 538938--538966 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
538928 CATGCGATAA
538938 TGGTACTTTTGTTTC
1 TGGTACTTTTGTTTC
538953 TGGTACTTTTGTTT
1 TGGTACTTTTGTTT
538967 AACCCACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.21, T:0.62
Consensus pattern (15 bp):
TGGTACTTTTGTTTC
Found at i:538962 original size:67 final size:67
Alignment explanation
Indices: 538886--539018 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
538876 CCCTCGATAT
* *
538886 TGGTACTTTTATTTAACCCACGATTA-TGACACTTTTGTTTAACATGCGATAATGGTACTTTTGT
1 TGGTACTTTTATTTAACCCACGA-TACTGAAACTTTTGTTTAACATACGATAATGGTACTTTTGT
538950 TTC
65 TTC
* *
538953 TGGTACTTTTGTTTAACCCACGATACTGAAACTTTTGTTTAACATACGATACTGGTACTTTTGTT
1 TGGTACTTTTATTTAACCCACGATACTGAAACTTTTGTTTAACATACGATAATGGTACTTTTGTT
539018 T
66 T
539019 AACATACGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 2 0.03
67 59 0.97
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (67 bp):
TGGTACTTTTATTTAACCCACGATACTGAAACTTTTGTTTAACATACGATAATGGTACTTTTGTT
TC
Done.