Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold256
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1244454
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 8
Found at i:225975 original size:28 final size:27
Alignment explanation
Indices: 225929--225998 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
225919 ACCCTTTTTG
*
225929 TTGTTTTTTGTTTGTTTGTTTGTTTGTT
1 TTGTTTTTT-TTTTTTTGTTTGTTTGTT
*
225957 TTTTTTTCTTTTTTTTTGTTTGTTTGTT
1 TTGTTTT-TTTTTTTTTGTTTGTTTGTT
225985 TTGTTTTTTTTTTT
1 TTGTTTTTTTTTTT
225999 GTGGAGGACG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.18
28 29 0.76
29 2 0.05
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.84
Consensus pattern (27 bp):
TTGTTTTTTTTTTTTTGTTTGTTTGTT
Found at i:240524 original size:52 final size:52
Alignment explanation
Indices: 240382--240510 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
240372 CGAAATATGA
*
240382 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATAAATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATAAATCTAGGC
* * * *
240434 AAATTTGCCTGTATGTATCAATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATAAATCTAGGC
240486 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
240511 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATAAATCTAGGC
Found at i:240810 original size:39 final size:39
Alignment explanation
Indices: 240756--240834 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
240746 TTTTCGCCGG
*
240756 GCGCTGTTGGCACTCGACGAATTTATCCCCACATGTGTC
1 GCGCTGTTGGCACTCGACGAATTCATCCCCACATGTGTC
*
240795 GCGCTGTTGGCACTCGACGAATTCGTCCCCACATGTGTC
1 GCGCTGTTGGCACTCGACGAATTCATCCCCACATGTGTC
240834 G
1 G
240835 AACCTTCCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.16, C:0.32, G:0.25, T:0.27
Consensus pattern (39 bp):
GCGCTGTTGGCACTCGACGAATTCATCCCCACATGTGTC
Found at i:241615 original size:157 final size:158
Alignment explanation
Indices: 241433--241718 Score: 418
Period size: 157 Copynumber: 1.8 Consensus size: 158
241423 TATTATAGTA
**
241433 AAAATTAAATATTAATCATTTTTTTAATATTTTATATTCATATGGGAATTTATAAGGG-TATAAA
1 AAAATTAAATATTAATCATTTTTTTAATATTTTATATTCATATGGGAATCCAT-AGGGATATAAA
** *
241497 AGATTTC-AAAACTTTTCGTATCTTTTCGGGTTTTTATTATGGTACGAAATGGCAT-TTTTCAAG
65 AGATTTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATTAAGGTACGAAAT-G-ATATTTTCAAG
241560 AATAAAAAAATAAATTGACACTTTCATAATC
128 AATAAAAAAATAAATTGACACTTTCATAATC
* * * *
241591 AAAA-TAAATGTTAATCATTTTTTTAATCTTTTATATTCCTATGGGAATCCGTAGGGATATAAAA
1 AAAATTAAATATTAATCATTTTTTTAATATTTTATATTCATATGGGAATCCATAGGGATATAAAA
* *
241655 GATTTCAAAAACTTTTCGTATCTTTTTGGGTTTCCATTAAGGTATGAAATGATATTTTCAAGAA
66 GATTTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATTAAGGTACGAAATGATATTTTCAAGAA
241719 AGAGATTTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
156 6 0.05
157 66 0.58
158 42 0.37
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (158 bp):
AAAATTAAATATTAATCATTTTTTTAATATTTTATATTCATATGGGAATCCATAGGGATATAAAA
GATTTCAAAAACTTTTCGTATCTTTTCGGGTTTCCATTAAGGTACGAAATGATATTTTCAAGAAT
AAAAAAATAAATTGACACTTTCATAATC
Found at i:244490 original size:72 final size:71
Alignment explanation
Indices: 244365--244588 Score: 251
Period size: 72 Copynumber: 3.1 Consensus size: 71
244355 GAATAGAGTG
* * *
244365 ATGCCACCAG-CTTGTGTGGCTTT-GAAAGA-AAAAAACGTCTTGCTTTTTGAGGACTGGAAAAG
1 ATGCCACCAGCCTTGTG-GGCTTTGGAAAAAGAAAAAACATCATGCTTTTTGAGGACTGGAAAAG
244427 ATAAATT
65 ATAAATT
* * *
244434 ATGCCACCAGCCTCTGTGGGCTTTGGAAAAAGAAAAAACATCCTACTTTTTAAGGACTGGAAAAG
1 ATGCCACCAGCCT-TGTGGGCTTTGGAAAAAGAAAAAACATCATGCTTTTTGAGGACTGGAAAAG
*
244499 ATAAATG
65 ATAAATT
* * *
244506 ATGCCACCAG-CTTGTGTAGGCTTTGAAGAAAAAGAAAAAGCATTATGCTCTTTGAGGACTGGAA
1 ATGCCACCAGCCTTGTG--GGCTTTG--GAAAAAGAAAAAACATCATGCTTTTTGAGGACTGGAA
*
244570 AATAT-AATT
62 AAGATAAATT
244579 GATGCCACCA
1 -ATGCCACCA
244589 ATTTGTTTGG
Statistics
Matches: 132, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
69 10 0.08
70 12 0.09
71 11 0.08
72 52 0.39
73 3 0.02
74 44 0.33
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (71 bp):
ATGCCACCAGCCTTGTGGGCTTTGGAAAAAGAAAAAACATCATGCTTTTTGAGGACTGGAAAAGA
TAAATT
Found at i:244582 original size:74 final size:73
Alignment explanation
Indices: 244363--244693 Score: 288
Period size: 74 Copynumber: 4.6 Consensus size: 73
244353 GAGAATAGAG
* * *
244363 TGATGCCACCAGCTTGTGTGGCTTTG-A-AAGAA-AAAAA-CGTCT-TGCTTTTTGAGGACTGGA
1 TGATGCCACCAGCTTGTGTGGCTTTGAAGAAAAAGAAAAAGCAT-TATGCTCTTTGAGGACTGGA
244423 AAAGATAAAT
65 AAAGAT-AAT
* ** * * *
244433 T-ATGCCACCAGCCTCTGTG-GGCTTTG--GAAAAAGAAAAAACATCCTACTTTTTAAGGACTGG
1 TGATGCCACCAG-CT-TGTGTGGCTTTGAAGAAAAAGAAAAAGCATTATGCTCTTTGAGGACTGG
*
244494 AAAAGATAAA
64 AAAAGATAAT
244504 TGATGCCACCAGCTTGTGTAGGCTTTGAAGAAAAAGAAAAAGCATTATGCTCTTTGAGGACTGGA
1 TGATGCCACCAGCTTGTGT-GGCTTTGAAGAAAAAGAAAAAGCATTATGCTCTTTGAGGACTGGA
*
244569 AAATATAAT
65 AAAGATAAT
** * * * * *
244578 TGATGCCACCAATTTGTTTGGGCTTTGAAAAAAAAAGAAAAGGC-TTATTGCTCTTTGAAGACTA
1 TGATGCCACCAGCTTGTGT-GGCTTTG-AAGAAAAAGAAAAAGCATTA-TGCTCTTTGAGGACTG
* *
244642 GCAAAGATAAG
63 GAAAAGATAAT
* * * *
244653 TAATACCACCAACTTGTGTGGACTTTGAAGAAGAA-AAAAAG
1 TGATGCCACCAGCTTGTGTGG-CTTTGAAGAAAAAGAAAAAG
244694 GCATCCAGCT
Statistics
Matches: 215, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
69 10 0.05
70 18 0.08
71 14 0.07
72 41 0.19
73 5 0.02
74 71 0.33
75 56 0.26
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (73 bp):
TGATGCCACCAGCTTGTGTGGCTTTGAAGAAAAAGAAAAAGCATTATGCTCTTTGAGGACTGGAA
AAGATAAT
Found at i:244662 original size:75 final size:75
Alignment explanation
Indices: 244488--244697 Score: 210
Period size: 75 Copynumber: 2.8 Consensus size: 75
244478 ACTTTTTAAG
* * * * * * * *
244488 GACTGGAAAAGATAAATGATGCCACCAGCTTGTGTAGGCTTTG-AAGAAAAAGAAAAAGCATTAT
1 GACTAGAAAAGATAAGTAATACCACCAACTTGTGTGGGCTTTGAAAAAAAAAGAAAAGGCATTAT
*
244552 GCTCTTTGAG
66 GCTCTTTGAA
* * * * * * *
244562 GACTGGAAAATATAATTGATGCCACCAATTTGTTTGGGCTTTGAAAAAAAAAGAAAAGGC-TTAT
1 GACTAGAAAAGATAAGTAATACCACCAACTTGTGTGGGCTTTGAAAAAAAAAGAAAAGGCATTA-
244626 TGCTCTTTGAA
65 TGCTCTTTGAA
* * * *
244637 GACTAGCAAAGATAAGTAATACCACCAACTTGTGTGGACTTTGAAGAAGAAA-AAAAGGCAT
1 GACTAGAAAAGATAAGTAATACCACCAACTTGTGTGGGCTTTGAAAAAAAAAGAAAAGGCAT
244698 CCAGCTTTTT
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
74 47 0.42
75 66 0.58
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (75 bp):
GACTAGAAAAGATAAGTAATACCACCAACTTGTGTGGGCTTTGAAAAAAAAAGAAAAGGCATTAT
GCTCTTTGAA
Found at i:246544 original size:11 final size:11
Alignment explanation
Indices: 246512--246553 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
246502 TAAAGTAACA
246512 TTTATTAGTTAT
1 TTTATTA-TTAT
246524 TTTATT-TTAT
1 TTTATTATTAT
246534 TTTATTATTAT
1 TTTATTATTAT
*
246545 TTTTTTATT
1 TTTATTATT
246554 TTGAAAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.36
11 12 0.43
12 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:249414 original size:25 final size:24
Alignment explanation
Indices: 249360--249407 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
249350 CTCGATGAAT
*
249360 AAATTTTGATATTTTTTATGAAAG
1 AAATTTTGATATTTTTTAGGAAAG
249384 AAATTTTGATATTTTTTAAGGAAA
1 AAATTTTGATATTTTTT-AGGAAA
249408 AGCATTTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (24 bp):
AAATTTTGATATTTTTTAGGAAAG
Found at i:250719 original size:43 final size:42
Alignment explanation
Indices: 250671--250792 Score: 122
Period size: 43 Copynumber: 2.9 Consensus size: 42
250661 AAAAAGTTGA
*
250671 TTGGGATTGAATCGACAAGCCAACAAAGGATAGAAAGATTCAC
1 TTGGGATT-AATCGACAAGTCAACAAAGGATAGAAAGATTCAC
* * * * *
250714 TTGGGATTAAGCCGACAGGTAAACAAGGGAT-GAAAGATTGAC
1 TTGGGATTAA-TCGACAAGTCAACAAAGGATAGAAAGATTCAC
* * *
250756 -TGGGATTTAATCGACAAGTCAAGAAAAGATAAAAAGA
1 TTGGGA-TTAATCGACAAGTCAACAAAGGATAGAAAGA
250793 CTTAACCAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
41 19 0.30
42 21 0.33
43 23 0.37
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.19
Consensus pattern (42 bp):
TTGGGATTAATCGACAAGTCAACAAAGGATAGAAAGATTCAC
Found at i:250792 original size:42 final size:42
Alignment explanation
Indices: 250656--250792 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 42
250646 GGTAAATAAT
* * *
250656 GGATAAAAA-AGTTGATTGGGATTGAATCGACAAGCCAACAAA
1 GGATAAAAAGA-TTGACTGGGATTTAATCGACAAGTCAACAAA
* * * * * *
250698 GGATAGAAAGATTCACTTGGGA-TTAAGCCGACAGGTAAACAAG
1 GGATAAAAAGATTGAC-TGGGATTTAA-TCGACAAGTCAACAAA
* *
250741 GGAT-GAAAGATTGACTGGGATTTAATCGACAAGTCAAGAAA
1 GGATAAAAAGATTGACTGGGATTTAATCGACAAGTCAACAAA
*
250782 AGATAAAAAGA
1 GGATAAAAAGA
250793 CTTAACCAAT
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
41 19 0.26
42 33 0.45
43 21 0.29
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.19
Consensus pattern (42 bp):
GGATAAAAAGATTGACTGGGATTTAATCGACAAGTCAACAAA
Found at i:250900 original size:44 final size:43
Alignment explanation
Indices: 250834--250929 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 43
250824 GATCAGGACT
* * * *
250834 AAACCATCACGTCGAGCGAAGATAATAAAAGTTTGACCAGGGAA
1 AAACCATCACATCCAACAAAGATAA-AAAAGTTTGACCAGGGAA
** * **
250878 AAACCATCACATCCAACAAAGATAAAAGGGTTTGACTAGGGCG
1 AAACCATCACATCCAACAAAGATAAAAAAGTTTGACCAGGGAA
250921 AAACCATCA
1 AAACCATCA
250930 TGTCAAATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 22 0.51
44 21 0.49
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.16
Consensus pattern (43 bp):
AAACCATCACATCCAACAAAGATAAAAAAGTTTGACCAGGGAA
Found at i:250993 original size:47 final size:46
Alignment explanation
Indices: 250931--251048 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
250921 AAACCATCAT
* * ** *
250931 GTCAAATAAGGATGAAAAGGGGTTTGA-CTATTGTGATAATCGATATA
1 GTCAAACAAGAATGAAAA-GGGTTTGAGC-AGAGTGATAATCGATACA
* *
250978 GTCAAACAAGAATGAAAAGGGTTTAAGCAGAGTGGTAATCGATACA
1 GTCAAACAAGAATGAAAAGGGTTTGAGCAGAGTGATAATCGATACA
*
251024 GTCAAACAAGAAAGAAAAGGGTTTG
1 GTCAAACAAGAATGAAAAGGGTTTG
251049 TTTGGTAAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 44 0.72
47 17 0.28
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.23
Consensus pattern (46 bp):
GTCAAACAAGAATGAAAAGGGTTTGAGCAGAGTGATAATCGATACA
Found at i:251696 original size:61 final size:61
Alignment explanation
Indices: 251596--251723 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
251586 AAAGATGATG
* * * * * **
251596 AAGATGAGAAGAGTGATAAAGGTGCCAATATGCTGATTCATGGCCAGCGATATTGGGTTTA
1 AAGATGAGAAGACTGATAAAGGTGCCAACATGCTAATTCAAGGCCAGCAATATTGGGCATA
* *
251657 AAGATGAGAAGACTGATAAAGGTGTCAACATGTTAATTCAAGGCCAGCAATATTGGGCATA
1 AAGATGAGAAGACTGATAAAGGTGCCAACATGCTAATTCAAGGCCAGCAATATTGGGCATA
251718 AAGATG
1 AAGATG
251724 CAAAGAATGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (61 bp):
AAGATGAGAAGACTGATAAAGGTGCCAACATGCTAATTCAAGGCCAGCAATATTGGGCATA
Found at i:251852 original size:52 final size:50
Alignment explanation
Indices: 251796--251916 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 50
251786 ATTTAAAGCT
*
251796 AGCGAAATTGGGCTTAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCC
1 AGCGAAATTGGGCTTA-GAA-GATAAAGATGCCAATATGCTGATTCAAGGCC
* * * * * * *
251848 AGCGACATTGGACTTA-AAGATGAAGGTGCCAATGTGCTGGTTTAAGGCC
1 AGCGAAATTGGGCTTAGAAGATAAAGATGCCAATATGCTGATTCAAGGCC
251897 AGC-AACATTGGGCTTAGAAG
1 AGCGAA-ATTGGGCTTAGAAG
251917 TAGATGCCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.02
49 37 0.65
50 5 0.09
52 14 0.25
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (50 bp):
AGCGAAATTGGGCTTAGAAGATAAAGATGCCAATATGCTGATTCAAGGCC
Found at i:251980 original size:31 final size:32
Alignment explanation
Indices: 251921--251989 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
251911 TAGAAGTAGA
* * *
251921 TGCCACCAATTTGTGTGGGCTTTTGAAAAGGT
1 TGCCACCAACTTGTGCGGACTTTTGAAAAGGT
*
251953 TGCCACCAACTTGTGCGGAC-TTTGAAAATGT
1 TGCCACCAACTTGTGCGGACTTTTGAAAAGGT
251984 TGCCAC
1 TGCCAC
251990 AGAGTCGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGCGGACTTTTGAAAAGGT
Found at i:252014 original size:27 final size:27
Alignment explanation
Indices: 251984--252453 Score: 455
Period size: 27 Copynumber: 17.2 Consensus size: 27
251974 TTGAAAATGT
* *
251984 TGCCACAGAGTCGTGGACTTAAAAGTG
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
* *
252011 TGCCACATAGTCGTAGGCTTAAAAGGGG
1 TGCCACAGAGTCGTGGGCTTAAAA-GGG
*
252039 TGCCATAGAGTCGTGGGCTTAAAAGGG
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
*
252066 TGCCACAGAGTCGTGGGCTTAAAAAGG
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
* ** *
252093 TACCATGGAGTTGTGGGCTTAAAAGGGG
1 TGCCACAGAGTCGTGGGCTTAAAA-GGG
*
252121 TGCCACAGAGTCGTGGGGTTAAAAGGGG
1 TGCCACAGAGTCGTGGGCTTAAAA-GGG
** *
252149 TGCCATGGAGTTGTGGGCTTAAAAGGG
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
* * *
252176 TGCCACGGAGTCGCGGGCTTAAAAGGT
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
* * *
252203 TGCCACAAAGTCATGGACTTAAAAGGG
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
*
252230 TGCCACAGAGTCGTGGGCTTAAAAAGG
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
* ** * * *
252257 TACCATGGAGTCATGGACTTAAAAGGA
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
* * *
252284 TGCCACGGAGTCATGGGCTTAAAAGGT
1 TGCCACAGAGTCGTGGGCTTAAAAGGG
*
252311 TGCCTCAGAGTCGTGGGCTTAAAAGGGG
1 TGCCACAGAGTCGTGGGCTTAAAA-GGG
*
252339 TGCCAC-GAAGTCATGGGCTTAAAAGGGG
1 TGCCACAG-AGTCGTGGGCTTAAAA-GGG
*
252367 TGCCACGGAGTCGTGGGCTTGAAAA-GG
1 TGCCACAGAGTCGTGGGCTT-AAAAGGG
* * ** *
252394 TACCA-TGAAGTCGTGGATTTAAAAGGA
1 TGCCACAG-AGTCGTGGGCTTAAAAGGG
* *
252421 TGCCACTA-ATTTGT-GGCTTAAAAGGGG
1 TGCCAC-AGAGTCGTGGGCTTAAAA-GGG
252448 TGCCAC
1 TGCCAC
252454 TGACTTGTGA
Statistics
Matches: 365, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
26 12 0.03
27 237 0.65
28 111 0.30
29 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (27 bp):
TGCCACAGAGTCGTGGGCTTAAAAGGG
Found at i:252135 original size:137 final size:134
Alignment explanation
Indices: 251986--252452 Score: 494
Period size: 137 Copynumber: 3.4 Consensus size: 134
251976 GAAAATGTTG
** *
251986 CCACAGAGTCGTGGACTTAAAAGTG-TGCCACATAGTCGTAGGCTTAAAAGGGGTGCCATAGAGT
1 CCACAGAGTCGTGGACTTAAAAG-GATGCCACGGAGTCGTGGGCTTAAAA-GGGTGCCATAGAGT
* * * * *
252050 CGTGGGCTTAAAAGGGTGCCACAGAGTCGTGGGCTTAAAAAGGTACCATGGAGTTGTGGGCTTAA
64 CGTGGGCTTAAAAGGGTGCCACAGAGTCATGGGCTTAAAAGGGTGCCACGGAGTCGTGGGCTTAA
*
252115 AAGGGGTG
129 AA--GGTA
** * * * **
252123 CCACAGAGTCGTGGGGTTAAAAGGGGTGCCATGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTC
1 CCACAGAGTCGTGGACTTAAAA-GGATGCCACGGAGTCGTGGGCTTAAAAGGGTGCCATAGAGTC
* * * * *
252188 GCGGGCTTAAAAGGTTGCCACAAAGTCATGGACTTAAAAGGGTGCCACAGAGTCGTGGGCTTAAA
65 GTGGGCTTAAAAGGGTGCCACAGAGTCATGGGCTTAAAAGGGTGCCACGGAGTCGTGGGCTT-AA
252253 AAGGTA
129 AAGGTA
** * * *
252259 CCATGGAGTCATGGACTTAAAAGGATGCCACGGAGTCATGGGCTTAAAAGGTTGCC-TCAGAGTC
1 CCACAGAGTCGTGGACTTAAAAGGATGCCACGGAGTCGTGGGCTTAAAAGGGTGCCAT-AGAGTC
252323 GTGGGCTTAAAAGGGGTGCCAC-GAAGTCATGGGCTTAAAAGGGGTGCCACGGAGTCGTGGGCTT
65 GTGGGCTTAAAA-GGGTGCCACAG-AGTCATGGGCTTAAAA-GGGTGCCACGGAGTCGTGGGCTT
252387 GAAAAGGTA
127 -AAAAGGTA
* * ** * *
252396 CCA-TGAAGTCGTGGATTTAAAAGGATGCCACTAATTTGT-GGCTTAAAAGGGGTGCCA
1 CCACAG-AGTCGTGGACTTAAAAGGATGCCACGGAGTCGTGGGCTTAAAA-GGGTGCCA
252453 CTGACTTGTG
Statistics
Matches: 273, Mismatches: 47, Indels: 19
0.81 0.14 0.06
Matches are distributed among these distances:
135 45 0.16
136 53 0.19
137 151 0.55
138 24 0.09
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (134 bp):
CCACAGAGTCGTGGACTTAAAAGGATGCCACGGAGTCGTGGGCTTAAAAGGGTGCCATAGAGTCG
TGGGCTTAAAAGGGTGCCACAGAGTCATGGGCTTAAAAGGGTGCCACGGAGTCGTGGGCTTAAAA
GGTA
Found at i:252483 original size:28 final size:27
Alignment explanation
Indices: 252406--252496 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
252396 CCATGAAGTC
* * *
252406 GTGGATTTAAAAGGATGCCACTAATTT
1 GTGGCTTTAAAAGGATGCCACTGACTT
*
252433 GTGGC-TTAAAAGGGGTGCCACTGACTT
1 GTGGCTTTAAAA-GGATGCCACTGACTT
*
252460 GTGAGCTTTAAAAGGATGCGACTGACTT
1 GTG-GCTTTAAAAGGATGCCACTGACTT
252488 GTGGGCTTT
1 GT-GGCTTT
252497 GGAAAGTAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
26 6 0.11
27 19 0.35
28 22 0.41
29 7 0.13
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (27 bp):
GTGGCTTTAAAAGGATGCCACTGACTT
Found at i:253961 original size:7 final size:7
Alignment explanation
Indices: 253947--253997 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
253937 ATCCAGACCC
253947 TTTTTGT
1 TTTTTGT
*
253954 TGTTTGT
1 TTTTTGT
253961 TTTTTGT
1 TTTTTGT
253968 TTTTT-T
1 TTTTTGT
253974 TTTTTGT
1 TTTTTGT
253981 TTTTTGT
1 TTTTTGT
253988 TTTTTGT
1 TTTTTGT
253995 TTT
1 TTT
253998 CTTTTGTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 6 0.15
7 35 0.85
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTTGT
Found at i:253979 original size:20 final size:21
Alignment explanation
Indices: 253947--253997 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
253937 ATCCAGACCC
*
253947 TTTTTGTTGTTTGTTTTTTGT
1 TTTTTGTTTTTTGTTTTTTGT
253968 TTTTT-TTTTTTGTTTTTTGT
1 TTTTTGTTTTTTGTTTTTTGT
253988 TTTTTGTTTT
1 TTTTTGTTTT
253998 CTTTTGTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (21 bp):
TTTTTGTTTTTTGTTTTTTGT
Found at i:253986 original size:27 final size:28
Alignment explanation
Indices: 253947--254007 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
253937 ATCCAGACCC
253947 TTTTTGTTGTTTGTTTTTTGTTTT-TTT
1 TTTTTGTTGTTTGTTTTTTGTTTTCTTT
*
253974 TTTTTGTTTTTTGTTTTTTGTTTTCTTT
1 TTTTTGTTGTTTGTTTTTTGTTTTCTTT
*
254002 TGTTTG
1 TTTTTG
254008 CATAGGATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (28 bp):
TTTTTGTTGTTTGTTTTTTGTTTTCTTT
Found at i:254007 original size:14 final size:13
Alignment explanation
Indices: 253947--254007 Score: 77
Period size: 14 Copynumber: 4.5 Consensus size: 13
253937 ATCCAGACCC
*
253947 TTTTTGTTGTTTGT
1 TTTTTGTT-TTTTT
253961 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
253974 TTTTTGTTTTTTGT
1 TTTTTGTTTTTT-T
253988 TTTTTGTTTTCTTT
1 TTTTTGTTTT-TTT
*
254002 TGTTTG
1 TTTTTG
254008 CATAGGATGC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 16 0.37
14 25 0.58
15 2 0.05
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:264319 original size:14 final size:14
Alignment explanation
Indices: 264300--264333 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
264290 GGGCCCATCG
*
264300 CGGGTTTGATAAAT
1 CGGGTTTGAAAAAT
264314 CGGGTTTGAAAAAT
1 CGGGTTTGAAAAAT
*
264328 TGGGTT
1 CGGGTT
264334 CAATTCGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (14 bp):
CGGGTTTGAAAAAT
Found at i:269125 original size:49 final size:49
Alignment explanation
Indices: 269069--269572 Score: 556
Period size: 49 Copynumber: 10.2 Consensus size: 49
269059 GTTTGAAATG
* *
269069 TTGGACTTCAAGTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
1 TTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * *
269118 TTGGACTTAAAGAAGACAGAGGTGCCAATATGCTGATTCAAGGCCAGCAATA
1 TTGGACTTAAAG-ATA-A-AGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * * * *
269170 TTGGACTTCAAGCTGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACA
1 TTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * * *
269219 TTGGGTCTTAAAGATGAAGGTGCCAATGTGCTGATTTAAGGCCAGCGACA
1 TT-GGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
** * *
269269 TTGGACTTAAAGATGACAAAGGCACCAATATGCTGATTTAAGGCCAGCGATA
1 TTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * *
269321 TTGGACTTAGAA-ATGAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACA
1 TTGGACTTA-AAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * *
269370 TTGGTCTTAAAGATAAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACA
1 TTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * *
269419 TTAGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
1 TTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
*
269471 TTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
1 TTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * * *
269514 TTGGTCTTAAAGA-CAAGGTGCCAATATGCTAATTCAAGGCCAGTGACA
1 TTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
*
269562 TTGGGCTTAAA
1 TTGGACTTAAA
269573 AGAAGACGCC
Statistics
Matches: 386, Mismatches: 51, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
43 37 0.10
44 1 0.00
46 1 0.00
48 43 0.11
49 135 0.35
50 46 0.12
51 2 0.01
52 119 0.31
53 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
TTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
Found at i:269358 original size:151 final size:148
Alignment explanation
Indices: 269082--269572 Score: 731
Period size: 151 Copynumber: 3.3 Consensus size: 148
269072 GACTTCAAGT
* * *
269082 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGACAGAGGTGCCAAT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAAT
* *
269147 ATGCTGATTCAAGGCCAGCAATATTGGACTTCAAGCTGAAGGTGCCAATGTGCTGATTCAAGGCC
66 ATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-ATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
269212 AACGACATTGGGTCTTAAAGA
129 AGCGACATT-GGTCTTAAAGA
* * * *
269233 TGAAGGTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCACCAAT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAAT
* *
269298 ATGCTGATTTAAGGCCAGCGATATTGGACTTAGAAATGAAGGTGCCAATGTGCTGATTCAAGGCT
66 ATGCTGATTCAAGGCCAGCGATATTGGACTT--AAATGAAGGTGCCAATGTGCTGATTCAAGGCC
269363 AGCGACATTGGTCTTAAAGA
129 AGCGACATTGGTCTTAAAGA
* * *
269383 TAAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCGCCAAT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAAT
269448 ATGCTGATTCAAGGCCAGCGATATTGGACTT--A--AAGGTGCCAATGTGCTGATTCAAGGCCAG
66 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAATGAAGGTGCCAATGTGCTGATTCAAGGCCAG
269509 CGACATTGGTCTTAAAGA
131 CGACATTGGTCTTAAAGA
* * * *
269527 -CAAGGTGCCAATATGCTAATTCAAGGCCAGTGACATTGGGCTTAAA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
269573 AGAAGACGCC
Statistics
Matches: 312, Mismatches: 27, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
143 39 0.12
144 46 0.15
146 1 0.00
150 101 0.32
151 123 0.39
152 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (148 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAAT
ATGCTGATTCAAGGCCAGCGATATTGGACTTAAATGAAGGTGCCAATGTGCTGATTCAAGGCCAG
CGACATTGGTCTTAAAGA
Found at i:269361 original size:101 final size:98
Alignment explanation
Indices: 269069--269572 Score: 549
Period size: 101 Copynumber: 5.1 Consensus size: 98
269059 GTTTGAAATG
* * * * * *
269069 TTGGACTTCAAGTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAGA
1 TTGGACTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-
* *
269134 CAGAGGTGCCAATATGCTGATTCAAGGCCAGCAATA
65 -A-AGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * * * *
269170 TTGGACTTCAAGCTGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTCTTAAAGATG
1 TTGGACTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATG
* *
269235 AAGGTGCCAATGTGCTGATTTAAGGCCAGCGACA
65 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * * *
269269 TTGGACTTAAAGATGACAAAGGCACCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAGAA-
1 TTGGACTTAAAGATG---AAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA-AAG
* *
269333 ATGAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACA
62 ATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * *
269370 TTGGTCTTAAAGAT-AAAGCTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATG
1 TTGGACTTAAAGATGAAGGC-GCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
269434 ACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATA
65 ---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACA
* * *
269471 TTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CA
1 TTGGACTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
* *
269529 AGGTGCCAATATGCTAATTCAAGGCCAGTGACA
66 AGGTGCCAATATGCTGATTCAAGGCCAGCGACA
*
269562 TTGGGCTTAAA
1 TTGGACTTAAA
269573 AGAAGACGCC
Statistics
Matches: 347, Mismatches: 43, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
91 37 0.11
95 40 0.12
96 3 0.01
97 7 0.02
98 36 0.10
99 42 0.12
100 1 0.00
101 138 0.40
102 43 0.12
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (98 bp):
TTGGACTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
AGGTGCCAATATGCTGATTCAAGGCCAGCGACA
Found at i:269497 original size:43 final size:43
Alignment explanation
Indices: 269436--269572 Score: 166
Period size: 43 Copynumber: 3.1 Consensus size: 43
269426 TAAAGATGAC
* *
269436 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
269479 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
269522 AAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGTGACATTGGGCTT
1 ----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
269570 AAA
1 AAA
269573 AGAAGACGCC
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
43 41 0.51
44 1 0.01
47 1 0.01
48 38 0.47
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:269692 original size:33 final size:33
Alignment explanation
Indices: 269650--269990 Score: 252
Period size: 30 Copynumber: 10.3 Consensus size: 33
269640 CCACTGACAC
* *
269650 GTGGGCTTAAAAGGAGAAAGATGCCACGGAGTT
1 GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
* *
269683 GTGGACTTAAAAAGGAAAAAATGATGCCATGAAGTT
1 GTGGACTT-AAAAGG-AAAAA-GATGCCACGGAGTT
* * *
269719 ATGGACTTAAAAGG-AAAAGGTGCCATGGAGTT
1 GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
* *
269751 GTGGACTTAAAAAGAAAAAGATGCCATGGAGTT
1 GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
*
269784 GTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTT
1 GTGGACTTAAAAGGAAAAA-GATGCCACGGAGTT
* *
269818 GTGGACTTTGAAAAGAAAAAAG-TGCCACAGAGTT
1 GTGGAC-TT-AAAAGGAAAAAGATGCCACGGAGTT
* * * *
269852 GTGGGCTTTGAAGAAAAGAAAAAGGTGCCACAGAGTT
1 GTGGAC-TT--A-AAAGGAAAAAGATGCCACGGAGTT
* ** * * *
269889 GTGGGCTTTGAA-GAAAAA-ATGGCACTGAGTC
1 GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
* * * *
269920 GTGGACTT---TGGAAAGAGATGCCACTGAGTC
1 GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
* * * *
269950 GTGGACTT---TGGAAAGAGATGCCACTGAGTC
1 GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
269980 GTGGACTTAAA
1 GTGGACTTAAA
269991 GGAGGTATTT
Statistics
Matches: 264, Mismatches: 29, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.02
30 50 0.19
31 16 0.06
32 30 0.11
33 48 0.18
34 43 0.16
35 14 0.05
36 40 0.15
37 18 0.07
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (33 bp):
GTGGACTTAAAAGGAAAAAGATGCCACGGAGTT
Found at i:269832 original size:101 final size:101
Alignment explanation
Indices: 269650--269892 Score: 283
Period size: 101 Copynumber: 2.4 Consensus size: 101
269640 CCACTGACAC
* * * *
269650 GTGGGCTTAAAAGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAATGATGCCATGA
1 GTGGGCTTAAAAAGAAAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAAGGATGCCACGA
* * **
269715 AGTTATGGACTTAAAAGGAAAAGGTGCCATGGAGTT
66 AGTTATGGACTTAAAAGAAAAAAGTGCCACAGAGTT
* * * *
269751 GTGGACTTAAAAAGAAAAAGATGCCATGGAGTTGTGGACTT-AAAAGG-AAAAAGGGTGCCACGG
1 GTGGGCTTAAAAAGAAAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAAGGATGCCACGA
*
269814 AGTTGTGGACTTTGAAAAGAAAAAAGTGCCACAGAGTT
66 AGTTATGGAC-TT-AAAAGAAAAAAGTGCCACAGAGTT
* *
269852 GTGGGCTTTGAAGAAAAGAAAAAGGTGCCACAGAGTTGTGG
1 GTGGGC-TT--A-AAAAGAAAAAGATGCCACGGAGTTGTGG
269893 GCTTTGAAGA
Statistics
Matches: 119, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
99 21 0.18
100 8 0.07
101 62 0.52
102 2 0.02
104 1 0.01
105 25 0.21
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.20
Consensus pattern (101 bp):
GTGGGCTTAAAAAGAAAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAAGGATGCCACGA
AGTTATGGACTTAAAAGAAAAAAGTGCCACAGAGTT
Found at i:269852 original size:68 final size:67
Alignment explanation
Indices: 269650--269927 Score: 275
Period size: 68 Copynumber: 4.1 Consensus size: 67
269640 CCACTGACAC
* * *
269650 GTGGGCTTAAAAGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAATGATGCCA-TG
1 GTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAA-GAAAAAA-GATGCCACTG
269714 AAGTT
64 -AGTT
* *
269719 ATGGACTTAAAAGG-AAAAGGTGCCATGGAGTTGTGGACTTAAAAAG-AAAAAGATGCCA-TGGA
1 GTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAAGATGCCACT-GA
269781 GTT
65 GTT
* *
269784 GTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAAG-TGCCACAG
1 GTGGACTTAAAAGGAAAAA-GGTGCCACGGAGTTGTGGAC-TTAAAAAGAAAAAAGATGCCACTG
269848 AGTT
64 AGTT
* * * * ** *
269852 GTGGGCTTTGAAGAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTT-TGAAG-AAAAA-ATGGCAC
1 GTGGAC-TT--A-AAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAAGATGCCAC
*
269914 TGAGTC
62 TGAGTT
269920 GTGGACTT
1 GTGGACTT
269928 TGGAAAGAGA
Statistics
Matches: 179, Mismatches: 19, Indels: 24
0.81 0.09 0.11
Matches are distributed among these distances:
65 25 0.14
66 10 0.06
67 22 0.12
68 69 0.39
69 23 0.13
70 2 0.01
71 19 0.11
72 9 0.05
ACGTcount: A:0.37, C:0.11, G:0.31, T:0.21
Consensus pattern (67 bp):
GTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAAGATGCCACTGAG
TT
Found at i:269861 original size:34 final size:34
Alignment explanation
Indices: 269666--269935 Score: 209
Period size: 34 Copynumber: 7.9 Consensus size: 34
269656 TTAAAAGGAG
*
269666 AAAGATGCCACGGAGTTGTGGAC-TTAAAAAGGAAA
1 AAAG-TGCCACGGAGTTGTGGACTTTGAAAA-GAAA
* * * *
269701 AAATGATGCCATGAAGTTATGGAC-TT-AAAAGGAA
1 AAA-G-TGCCACGGAGTTGTGGACTTTGAAAAGAAA
* * *
269735 AAGGTGCCATGGAGTTGTGGAC-TTAAAAAG-AA
1 AAAGTGCCACGGAGTTGTGGACTTTGAAAAGAAA
*
269767 AAAGATGCCATGGAGTTGTGGAC-TT-AAAAGGAAA
1 AAAG-TGCCACGGAGTTGTGGACTTTGAAAA-GAAA
*
269801 AAGGGTGCCACGGAGTTGTGGACTTTGAAAAGAAA
1 AA-AGTGCCACGGAGTTGTGGACTTTGAAAAGAAA
* *
269836 AAAGTGCCACAGAGTTGTGGGCTTTGAAGAAAAGAAA
1 AAAGTGCCACGGAGTTGTGGACTTT---GAAAAGAAA
* * *
269873 AAGGTGCCACAGAGTTGTGGGCTTTG--AAGAAA
1 AAAGTGCCACGGAGTTGTGGACTTTGAAAAGAAA
* * * *
269905 AAA-TGGCACTGAGTCGTGGACTTTGGAAAGA
1 AAAGTGCCACGGAGTTGTGGACTTTGAAAAGA
269936 GATGCCACTG
Statistics
Matches: 203, Mismatches: 19, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
31 18 0.09
32 35 0.17
33 31 0.15
34 47 0.23
35 16 0.08
36 23 0.11
37 33 0.16
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.21
Consensus pattern (34 bp):
AAAGTGCCACGGAGTTGTGGACTTTGAAAAGAAA
Found at i:269905 original size:37 final size:35
Alignment explanation
Indices: 269666--269897 Score: 205
Period size: 33 Copynumber: 6.7 Consensus size: 35
269656 TTAAAAGGAG
*
269666 AAAGATGCCACGGAGTTGTGGAC-TTA-AAAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAGAAAA-G-AA
* * * * *
269701 AAATGATGCCATGAAGTTATGGAC-TT--AAAAGGA
1 AAA-GGTGCCACGGAGTTGTGGACTTTAGAAAAGAA
*
269734 AAAGGTGCCATGGAGTTGTGGAC-TTA-AAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAGAAAAGAA
* * *
269767 AAAGATGCCATGGAGTTGTGGAC-TTA-AAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAGAAAAGAA
269800 AAAGGGTGCCACGGAGTTGTGGACTTT-GAAAAGAA
1 AAA-GGTGCCACGGAGTTGTGGACTTTAGAAAAGAA
* * *
269835 AAAAGTGCCACAGAGTTGTGGGCTTTGAAGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTT--AGAAAAGAA
* *
269872 AAAGGTGCCACAGAGTTGTGGGCTTT
1 AAAGGTGCCACGGAGTTGTGGACTTT
269898 GAAGAAAAAA
Statistics
Matches: 172, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
32 19 0.11
33 44 0.26
34 39 0.23
35 18 0.10
36 19 0.11
37 33 0.19
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.21
Consensus pattern (35 bp):
AAAGGTGCCACGGAGTTGTGGACTTTAGAAAAGAA
Found at i:277831 original size:19 final size:19
Alignment explanation
Indices: 277807--277870 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
277797 AGCGATACAT
*
277807 TGTATCAATACAACACTTA
1 TGTATCGATACAACACTTA
277826 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
277839 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
277858 TGTATCGATACAA
1 TGTATCGATACAA
277871 TTTCTGTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:277840 original size:32 final size:32
Alignment explanation
Indices: 277799--277869 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
277789 AGCTTCGTAG
277799 CGATACATTGTATCAATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
*
277831 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
277863 CGATACA
1 CGATACA
277870 ATTTCTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCAATACAACACTTATGTAT
Found at i:277844 original size:13 final size:13
Alignment explanation
Indices: 277826--277850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277816 ACAACACTTA
277826 TGTATCGATACAT
1 TGTATCGATACAT
277839 TGTATCGATACA
1 TGTATCGATACA
277851 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:279646 original size:20 final size:20
Alignment explanation
Indices: 279593--279647 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
279583 AAATTCCCAG
**
279593 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
279613 ATGTATCGATACATTGTAT-A
1 ATGTATCGATACATTG-ATCA
279633 ATGTATCGATACATT
1 ATGTATCGATACATT
279648 TCCTTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:279690 original size:13 final size:13
Alignment explanation
Indices: 279672--279697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
279662 CAGGGCAGCT
279672 TTGTATCGATACA
1 TTGTATCGATACA
279685 TTGTATCGATACA
1 TTGTATCGATACA
279698 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:285454 original size:13 final size:13
Alignment explanation
Indices: 285436--285516 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
285426 GCTTCGTAGT
285436 GATACATTGTATC
1 GATACATTGTATC
*
285449 GATACAACTTATGTAGC
1 GATAC-A--T-TGTATC
285466 GATACATTGTATC
1 GATACATTGTATC
285479 GATACAACACTCATGTATC
1 GAT---ACA-T--TGTATC
285498 GATACATTGTATC
1 GATACATTGTATC
285511 GATACA
1 GATACA
285517 AATCGTTGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 20
0.72 0.03 0.26
Matches are distributed among these distances:
13 25 0.45
14 2 0.04
15 1 0.02
16 8 0.14
17 11 0.20
19 9 0.16
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:285501 original size:32 final size:31
Alignment explanation
Indices: 285431--285518 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 31
285421 CAGTAGCTTC
* *
285431 GTAGTGATACATTGTATCGATAC-AACTTAT
1 GTAGCGATACATTGTATCGATACAAACTCAT
285461 GTAGCGATACATTGTATCGATACAACACTCAT
1 GTAGCGATACATTGTATCGATACAA-ACTCAT
*
285493 GTATCGATACATTGTATCGATACAAA
1 GTAGCGATACATTGTATCGATACAAA
285519 TCGTTGAAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 22 0.42
31 2 0.04
32 29 0.55
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (31 bp):
GTAGCGATACATTGTATCGATACAAACTCAT
Found at i:286424 original size:13 final size:13
Alignment explanation
Indices: 286406--286431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286396 TACAGCAAGT
286406 ATGTATCGATACA
1 ATGTATCGATACA
286419 ATGTATCGATACA
1 ATGTATCGATACA
286432 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:290514 original size:15 final size:15
Alignment explanation
Indices: 290494--290524 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
290484 TAAAAATGTC
*
290494 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
290509 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
290524 C
1 C
290525 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:292620 original size:13 final size:13
Alignment explanation
Indices: 292602--292640 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
292592 ACATTTTTCT
292602 TTGTATCGATACA
1 TTGTATCGATACA
292615 TTGTATCGATACA
1 TTGTATCGATACA
292628 TTGTATCGATACA
1 TTGTATCGATACA
292641 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:295077 original size:21 final size:20
Alignment explanation
Indices: 295033--295085 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
295023 ACAATTCAAA
* **
295033 GTATCGATACATGTAGCAAT
1 GTATCGATACATGAAAAAAT
295053 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAA-AT
*
295074 GTATTGATACAT
1 GTATCGATACAT
295086 TTCTTGGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (20 bp):
GTATCGATACATGAAAAAAT
Found at i:295142 original size:13 final size:13
Alignment explanation
Indices: 295124--295149 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295114 TACAGCAAGT
295124 ATGTATCGATACA
1 ATGTATCGATACA
295137 ATGTATCGATACA
1 ATGTATCGATACA
295150 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:296283 original size:49 final size:50
Alignment explanation
Indices: 296117--296449 Score: 330
Period size: 52 Copynumber: 6.5 Consensus size: 50
296107 GTCAATGTGT
* * * * * * * *
296117 TGATTCACGGTCAACGACATTAGACTTGAAGATCAGAAGAATGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-AAG-GTGCCAATATGC
* ** **
296169 TGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACAAAGACGCCAATATGC
1 TGATTCAAGGCCAGCGACATT-GGACTTAAAGATG--AAAGGTGCCAATATGC
* *
296222 TGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAGGTGCCAATATGC
* * **
296271 TGATTTAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGTAAATATGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGATG--AAAGGTGCCAATATGC
* * *
296323 TGATTCAAGGCCAGCAATATTGGACTTAAAGATG-AAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAGGTGCCAATATGC
* *
296372 TGATTCAAAGCCAGCGACATTGGACTTAAAGATGACAAAGGGGCCAATATGC
1 TGATTCAAGGCCAGCGACATTGGACTTAAAGATG--AAAGGTGCCAATATGC
*
296424 TGATTCAAGGCCAAG-GATATTGGACT
1 TGATTCAAGGCC-AGCGACATTGGACT
296450 GGTATGGCCG
Statistics
Matches: 235, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
49 86 0.37
52 106 0.45
53 39 0.17
54 3 0.01
55 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (50 bp):
TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAGGTGCCAATATGC
Found at i:296332 original size:101 final size:101
Alignment explanation
Indices: 296158--296449 Score: 469
Period size: 101 Copynumber: 2.9 Consensus size: 101
296148 ATCAGAAGAA
* ** *
296158 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACAAAGACGCCAATATGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGACAAAGGCGCCAATATGCT
296223 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
65 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* **
296260 TGCCAATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGTAAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
*
296325 ATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
296361 TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGACTTAAAGATGACAAAGGGGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
296426 ATTCAAGGCCAAG-GATATTGGACT
66 ATTCAAGGCC-AGCGATATTGGACT
296450 GGTATGGCCG
Statistics
Matches: 175, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 143 0.82
102 32 0.18
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (101 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:297467 original size:12 final size:12
Alignment explanation
Indices: 297452--297500 Score: 73
Period size: 12 Copynumber: 4.1 Consensus size: 12
297442 TTGCACTCTC
297452 TTTTGTTTTTTT
1 TTTTGTTTTTTT
297464 TTTTG-TTTTTT
1 TTTTGTTTTTTT
*
297475 TTTTGTTTTGTT
1 TTTTGTTTTTTT
297487 TTTTGTTTTGTTT
1 TTTTGTTTT-TTT
297500 T
1 T
297501 GGTTGTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 11 0.33
12 19 0.58
13 3 0.09
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:297478 original size:23 final size:23
Alignment explanation
Indices: 297452--297512 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
297442 TTGCACTCTC
* *
297452 TTTTGTTTTTTTTTTTGTTTTTT
1 TTTTGTTTTGTTTTTTGTTTTGT
297475 TTTTGTTTTGTTTTTTGTTTTGT
1 TTTTGTTTTGTTTTTTGTTTTGT
* *
297498 TTTGGTTGTGTTTTT
1 TTTTGTTTTGTTTTT
297513 GACTTTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (23 bp):
TTTTGTTTTGTTTTTTGTTTTGT
Found at i:297512 original size:12 final size:12
Alignment explanation
Indices: 297452--297513 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 12
297442 TTGCACTCTC
*
297452 TTTT-GTTTTTT
1 TTTTGGTTTTGT
*
297463 TTTTTGTTTT-T
1 TTTTGGTTTTGT
*
297474 TTTTTGTTTTGT
1 TTTTGGTTTTGT
*
297486 TTTTTGTTTTG-
1 TTTTGGTTTTGT
*
297497 TTTTGGTTGTGT
1 TTTTGGTTTTGT
297509 TTTTG
1 TTTTG
297514 ACTTTTTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
11 24 0.52
12 22 0.48
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (12 bp):
TTTTGGTTTTGT
Found at i:303968 original size:20 final size:20
Alignment explanation
Indices: 303943--304008 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
303933 TTTACCTGTA
303943 TGTATCGATACAAAGATTAG
1 TGTATCGATACAAAGATTAG
303963 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATTAG
303976 TGTATCGATACAAAGATTAG
1 TGTATCGATACAAAGATTAG
303996 TGTATCGATACAA
1 TGTATCGATACAA
304009 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 24 0.62
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAGATTAG
Found at i:303981 original size:13 final size:13
Alignment explanation
Indices: 303963--304020 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
303953 CAAAGATTAG
303963 TGTATCGATACAA
1 TGTATCGATACAA
303976 TGTATCGATACAA
1 TGTATCGATACAA
* *
303989 ---A--GAT-TAG
1 TGTATCGATACAA
303996 TGTATCGATACAA
1 TGTATCGATACAA
304009 TGTATCGATACA
1 TGTATCGATACA
304021 TTTGGGTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
10 2 0.06
12 3 0.09
13 26 0.74
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:303984 original size:33 final size:33
Alignment explanation
Indices: 303942--304020 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
303932 ATTTACCTGT
303942 ATGTATCGATACAAAGATTAGTGTATCGATACA
1 ATGTATCGATACAAAGATTAGTGTATCGATACA
303975 ATGTATCGATACAAAGATTAGTGTATCGATACA
1 ATGTATCGATACAAAGATTAGTGTATCGATACA
304008 ATGTATCGATACA
1 ATGTATCGATACA
304021 TTTGGGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGATTAGTGTATCGATACA
Found at i:304079 original size:13 final size:13
Alignment explanation
Indices: 304061--304129 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 13
304051 CAGTAGCTTC
304061 GTATCGATACATT
1 GTATCGATACATT
*
304074 GTATCGATACTTT
1 GTATCGATACATT
*
304087 GTATCAATACAACACTCAT
1 GTATCGAT---ACA-T--T
304106 GTATCGATACATT
1 GTATCGATACATT
304119 GTATCGATACA
1 GTATCGATACA
304130 AATCGTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
13 31 0.67
15 1 0.02
16 5 0.11
17 1 0.02
19 8 0.17
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:304899 original size:10 final size:10
Alignment explanation
Indices: 304884--304913 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
304874 TTTCATTTGA
304884 TTTTTTTTAC
1 TTTTTTTTAC
304894 TTTTTTTTAC
1 TTTTTTTTAC
*
304904 ATTTTTTTAC
1 TTTTTTTTAC
304914 GCATAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTTTAC
Found at i:308357 original size:165 final size:165
Alignment explanation
Indices: 308163--308795 Score: 660
Period size: 165 Copynumber: 3.9 Consensus size: 165
308153 AATACGGAGT
* *
308163 TTTTTTCT-TTGTAAACTTTTTTGGGAGGATTTTCATTAGTTTTTAATTTTTAAAATTCATCAAA
1 TTTTTTCTCTCGTAAACTTTTTT-GGAGGATTTTCATTAGTTTTTAATTTTTAAAATTCATAAAA
** * *
308227 TATTATTATTTAATTCATATTAAATCAATTTTTAAAAATTCATTCATTTTTATAGATTTTTGAAT
65 TATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTTTCATAGATTTTTGAAT
* *
308292 TTGTTCCTTGAAACTATCTTTTTTTTGAAATACCAAG
130 TTTTTCCTTGAAACT-TCTTTTTTTTGAAATACAAAG
* *
308329 TTCTTTTCTCT-GT-AA-TTTTTTAGGAGGATTTTTATTGGTTTTTAATTTTTAAAATTCATAAA
1 TT-TTTTCTCTCGTAAACTTTTTT-GGAGGATTTTCATTAGTTTTTAATTTTTAAAATTCATAAA
*
308391 ATATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTTTCATGGATTTTTGAA
64 ATATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTTTCATAGATTTTTGAA
* * *
308456 TTTTTTCCCTGAAACTCCCTTTTTTTGAAATACAAAG
129 TTTTTTCCTTGAAACTTCTTTTTTTTGAAATACAAAG
* *
308493 TTTCTTCT-TCGT-AA----TTT------CTTTCATTA-TCTTTTAA-TTTTAAAATTCATAAAA
1 TTTTTTCTCTCGTAAACTTTTTTGGAGGATTTTCATTAGT-TTTTAATTTTTAAAATTCATAAAA
* * * * * *
308544 TATTATTATTTAATTTAGATTAAGTCAGCTATCAAAAATTCATTCATTTTAATGGATTTTTGAAT
65 TATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTTTCATAGATTTTTGAA-
* * *
308609 TTTTTTCCTTGAAACTCCCCCTTTTTTTTTTCAAAATATAGAA-
129 TTTTTTCCTTGAAACT-----TCTTTTTTTT-GAAATACA-AAG
* * * *
308652 TTTTTTC-CTTCGTAAACTTTTTTGAAAGGATTTTCATTGGTTTTTAATTTTTAAAATTAATTAA
1 TTTTTTCTC-TCGTAAACTTTTTTG-GAGGATTTTCATTAGTTTTTAATTTTTAAAATTCATAAA
* * * * *
308716 ATATCATTATTTAATTTATATTAAATCAGTTTTCAAAAAATTCAATCATTTTCACCAG-TTTTTG
64 ATATTATTATTTAATTCATATTAAATCAGCTTTC-AAAAATTCATTCATTTTCA-TAGATTTTTG
308780 AATTTTTTCCTTGAAA
127 AATTTTTTCCTTGAAA
308796 TTTTCCTTTT
Statistics
Matches: 394, Mismatches: 43, Indels: 53
0.80 0.09 0.11
Matches are distributed among these distances:
152 77 0.20
153 27 0.07
158 7 0.02
159 12 0.03
160 9 0.02
161 2 0.01
162 1 0.00
163 9 0.02
164 20 0.05
165 120 0.30
166 4 0.01
167 8 0.02
168 1 0.00
172 13 0.03
173 58 0.15
174 25 0.06
175 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (165 bp):
TTTTTTCTCTCGTAAACTTTTTTGGAGGATTTTCATTAGTTTTTAATTTTTAAAATTCATAAAAT
ATTATTATTTAATTCATATTAAATCAGCTTTCAAAAATTCATTCATTTTCATAGATTTTTGAATT
TTTTCCTTGAAACTTCTTTTTTTTGAAATACAAAG
Found at i:309427 original size:21 final size:21
Alignment explanation
Indices: 309402--309469 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
309392 GGTCAGCTGA
309402 AAAGAAAGAGAAAAAAAAGAG
1 AAAGAAAGAGAAAAAAAAGAG
*
309423 AAAGAAAG-GCAAGAAAAAATAG
1 AAAGAAAGAG-AA-AAAAAAGAG
* *
309445 -AAGAAAATAGGAAAAAATAGAG
1 AAAG-AAAGA-GAAAAAAAAGAG
309467 AAA
1 AAA
309470 ACTAAGCTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
20 1 0.03
21 13 0.35
22 18 0.49
23 4 0.11
24 1 0.03
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.04
Consensus pattern (21 bp):
AAAGAAAGAGAAAAAAAAGAG
Found at i:315021 original size:21 final size:21
Alignment explanation
Indices: 314995--315047 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
314985 TTCAACAATT
314995 TGTATCGTTACAATAAGGT-AA
1 TGTATCGTTACAATAA-GTAAA
*
315016 TGTATCGATAC-ATAAGTAAA
1 TGTATCGTTACAATAAGTAAA
*
315036 TGTATCATTACA
1 TGTATCGTTACA
315048 TGTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 10 0.37
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (21 bp):
TGTATCGTTACAATAAGTAAA
Found at i:315188 original size:51 final size:50
Alignment explanation
Indices: 315104--315199 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 50
315094 TTTGGAAAGA
* * * *
315104 AAATGTATTGATACATTTTCATTACATTGATACATTTTGGATTTTGATCC
1 AAATATATTGATACATTTTCATTACATCGATACATTCTAGATTTTGATCC
**
315154 AAATATATTGATACATTCTTCATTGTATCGATACATTCTAGATTTT
1 AAATATATTGATACATT-TTCATTACATCGATACATTCTAGATTTT
315200 TGACCCAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 16 0.41
51 23 0.59
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (50 bp):
AAATATATTGATACATTTTCATTACATCGATACATTCTAGATTTTGATCC
Found at i:317105 original size:19 final size:20
Alignment explanation
Indices: 317060--317113 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
317050 CTACCAGTTT
* *
317060 CATGTATTGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
317080 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
317099 CATGTATCGATACAA
1 CATGTATCGATACAA
317114 AGCATAACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:325918 original size:19 final size:20
Alignment explanation
Indices: 325873--325925 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
325863 ACTGCTAGTT
*
325873 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
325893 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
325912 CATGTATCGATACA
1 CATGTATCGATACA
325926 TTATATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:326934 original size:5 final size:5
Alignment explanation
Indices: 326924--326961 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
326914 CATTTGTTAA
*
326924 TTATT TTATT TTATT TTATT ATTATT TTCTT TTATT TT
1 TTATT TTATT TTATT TTATT -TTATT TTATT TTATT TT
326962 CAAAAGTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:326939 original size:21 final size:21
Alignment explanation
Indices: 326921--326961 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
326911 TAACATTTGT
326921 TAATTATTTTATTTTATTTTA
1 TAATTATTTTATTTTATTTTA
* *
326942 TTATTATTTTCTTTTATTTT
1 TAATTATTTTATTTTATTTT
326962 CAAAAGTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TAATTATTTTATTTTATTTTA
Found at i:327811 original size:21 final size:22
Alignment explanation
Indices: 327785--327830 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
327775 TTTGCCTTAA
327785 TTTTTCTTTTT-TT-TCTCATTT
1 TTTTTCTTTTTATTATCTC-TTT
327806 TTTTTCTTTTTATTATCTCTTT
1 TTTTTCTTTTTATTATCTCTTT
327828 TTT
1 TTT
327831 CTTTATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.48
22 8 0.35
23 4 0.17
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTTTATTATCTCTTT
Found at i:328790 original size:166 final size:166
Alignment explanation
Indices: 328452--328864 Score: 460
Period size: 166 Copynumber: 2.5 Consensus size: 166
328442 AAACAAGGGC
* * **
328452 ATTTCATGGAAAATATGAAAAACTCATGAAAATAAATGTCTTTTTCAAAACTAATTTACTATGAA
1 ATTTCAAGGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTACTATGAA
* * ** *
328517 TTAATTGATGATATTTGATTAATATTAAAAATTTTTAACTGAGAAAAACCCTCCTGAAAACTTTT
66 TTAAATGATGATATTTGATGAATATTAAAAATTTCAAACTGAGAAAAACACTCCTGAAAACTTTT
** * * * *** * ***
328582 ATGGCATAGAAGACTCGATTTTTTGGAAATAGGGGC
131 ACAGCATAAAAAACTCGATATTTCAAAAATAAGAAA
* * *
328618 ATTTCAAGGAAAAAATAAAAAAGTCATGAAAATAAATGAATTTTTCAAAACTAACTTACTATGAA
1 ATTTCAAGGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTACTATGAA
328683 TTAAATGATGATATTTGATGAATATTAAAAATTTCAAACCT-AGAAAAACAC-CCTGGAAAA-TA
66 TTAAATGATGATATTTGATGAATATTAAAAATTTCAAA-CTGAGAAAAACACTCCT-GAAAACT-
328745 TTTACAG-AGTAAAAAACTTCG-TATTTCAAAAATAAGAAA
128 TTTACAGCA-TAAAAAAC-TCGATATTTCAAAAATAAGAAA
* * * * * *
328784 ATTTCAAGAAAAAAATGAAAAATTCATG-AAATAAATGGAATTTTTCAAAACTGATTTAATGTAA
1 ATTTCAAGGAAAAAATGAAAAACTCATGAAAATAAAT-GAATTTTTCAAAACTAATTTACTATGA
328848 ATTAAATGATGATATTT
65 ATTAAATGATGATATTT
328865 AAATAATTTT
Statistics
Matches: 209, Mismatches: 32, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
165 13 0.06
166 191 0.91
167 5 0.02
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (166 bp):
ATTTCAAGGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTACTATGAA
TTAAATGATGATATTTGATGAATATTAAAAATTTCAAACTGAGAAAAACACTCCTGAAAACTTTT
ACAGCATAAAAAACTCGATATTTCAAAAATAAGAAA
Found at i:328797 original size:21 final size:21
Alignment explanation
Indices: 328772--328819 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
328762 TTCGTATTTC
*
328772 AAAAATAAGAAAATTTCAAGA
1 AAAAATAAGAAAAATTCAAGA
* *
328793 AAAAA-ATGAAAAATTCATGA
1 AAAAATAAGAAAAATTCAAGA
328813 AATAAAT
1 AA-AAAT
328820 GGAATTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAAATAAGAAAAATTCAAGA
Found at i:328803 original size:20 final size:20
Alignment explanation
Indices: 328780--328820 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
328770 TCAAAAATAA
*
328780 GAAAATTTCAAGAAAAAAAT
1 GAAAAATTCAAGAAAAAAAT
* *
328800 GAAAAATTCATGAAATAAAT
1 GAAAAATTCAAGAAAAAAAT
328820 G
1 G
328821 GAATTTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (20 bp):
GAAAAATTCAAGAAAAAAAT
Found at i:329863 original size:21 final size:21
Alignment explanation
Indices: 329817--329866 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
329807 GACATATGGG
* *
329817 GATGCAAGTGCCTGCCTAGAT
1 GATGTAAGTGCCTACCTAGAT
329838 GATGTAAGTGCCTACCTAGAT
1 GATGTAAGTGCCTACCTAGAT
329859 GATGTAAG
1 GATGTAAG
329867 GTTAATGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (21 bp):
GATGTAAGTGCCTACCTAGAT
Found at i:331478 original size:80 final size:80
Alignment explanation
Indices: 331379--332046 Score: 578
Period size: 80 Copynumber: 8.3 Consensus size: 80
331369 GTAAAATTCG
* * * * * * *
331379 GTGTTTTAG-AGTAAAAATAGGGTTAGAGTATTCCCTAAAAAATGGTGGGGTTGGAGCATCCCCT
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
* *
331443 AATATGAAAATTTTG
66 AAGATGAAAATTTTA
* * ** * * * *
331458 GTGTTTTAGAAGTAAAAATAGGGTTGGAGTATTCTGTTGGAGATGATGGGGTTGAAGTATCCCCA
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
*
331523 AAGATGAAAAATTTA
66 AAGATGAAAATTTTA
* * *
331538 GTGTTTGAGAAATAAAAATGGGGTTGGAGTATCACCTTAGAGATGGTGGGGTTGGAGTAT-CCCT
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
*
331602 AAAGATGAAGAA-TTTG
66 -AAGATGAA-AATTTTA
** * * * * *
331618 GTGTTTGGGAAATAAAAATGGGGTTAGAGTATCCCCTTAAAAATGGTGCGGTTGGAGTATCCCCT
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
*
331683 AAGATGAAAATTTCA
66 AAGATGAAAATTTTA
*** * * ** * *
331698 GTGTTTTAGAAGTAAAAACCAGTTTGGAATATCCCCTCGGAGATGGTGGGGTTAGAGTATCCCTT
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
*
331763 AAAATGAAAATTTT-
66 AAGATGAAAATTTTA
* * * * * **
331777 GATGTTTTAAAAG-AAGAAACGAGGTTGGAGTATCCCCTTAGAGATGATGAGGTTAAAGTAT-CC
1 G-TGTTTTAGAAGTAA-AAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCC
*
331840 CTAAAGATGAAAAATTTA
64 CT-AAGATGAAAATTTTA
** * * * * * * * * *
331858 GTGTTTGGGAAATAAACATGGGGTTAGAGCATCCCCTTAAAAATGATGGGGTTAGAGTATCCTCT
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
* *
331923 GAGATGAAAACTTTA
66 AAGATGAAAATTTTA
* * * *
331938 GTGTTTTAAAAGTAAAAATGGGGATGGAGTATCCTCC-GAGAGATGGTGGGGTTGGAGAATCCCC
1 GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCC-CCTTAGAGATGGTGGGGTTGGAGTATCCCC
**
332002 T-AGATGAAAAATTCAA
65 TAAGATG-AAAATTTTA
* *
332018 TGTTTTTTGGAAGTAAAAACTGGGGTTGG
1 -GTGTTTTAGAAGTAAAAA-TGGGGTTGG
332047 TGTACCCTTT
Statistics
Matches: 472, Mismatches: 102, Indels: 27
0.79 0.17 0.04
Matches are distributed among these distances:
79 25 0.05
80 410 0.87
81 29 0.06
82 8 0.02
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (80 bp):
GTGTTTTAGAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAGATGGTGGGGTTGGAGTATCCCCT
AAGATGAAAATTTTA
Found at i:331818 original size:240 final size:239
Alignment explanation
Indices: 331390--332014 Score: 724
Period size: 240 Copynumber: 2.6 Consensus size: 239
331380 TGTTTTAGAG
* * * * *
331390 TAAAAATAGGGTTAGAGTATTCCCTAAAAAATGGTGGGGTTGGAGCATCCCCTAATATGAAAATT
1 TAAAAATGGGGTTAGAGTATCCCCTTAAAAATGGTGGGGTTGGAGTATCCCCTAAGATGAAAA-T
* * * * ** *
331455 TTGGTGTTTTAGAAGTAAAAATAGGGTTGGAGTATTCTGTTGGAGATGATGGGGTTGAAGTATCC
65 TTAGTGTTTTAGAAGTAAAAACAGGGTTGGAATATCCCCTCGGAGATGATGGGGTTGAAGTATCC
* * * *
331520 CCAAAGATGAAAAATTTAGTGTTTGAGAAATAAAAATGGGGTTGGAGTATCACCTTAGAGATGGT
130 CCAAAGATGAAAAATTTAGTGTTTGAGAAAGAAAAACGAGGTTGGAGTATCACCTTAGAGATGAT
* ** * *
331585 GGGGTTGGAGTATCCCTAAAGATGAAGAATTTGGTGTTTGGGAAA
195 GAGGTTAAAGTATCCCTAAAGATGAAAAATTTAGTGTTTGGGAAA
*
331630 TAAAAATGGGGTTAGAGTATCCCCTTAAAAATGGTGCGGTTGGAGTATCCCCTAAGATGAAAATT
1 TAAAAATGGGGTTAGAGTATCCCCTTAAAAATGGTGGGGTTGGAGTATCCCCTAAGATGAAAATT
* *
331695 TCAGTGTTTTAGAAGTAAAAACCA-GTTTGGAATATCCCCTCGGAGATGGTGGGGTT-AGAGTAT
66 T-AGTGTTTTAGAAGTAAAAA-CAGGGTTGGAATATCCCCTCGGAGATGATGGGGTTGA-AGTAT
* * * *
331758 CCCTTAAA-ATG-AAAATTTTGATGTTTTA-AAAGAAGAAACGAGGTTGGAGTATCCCCTTAGAG
128 CCC-CAAAGATGAAAAATTTAG-TGTTTGAGAAAGAA-AAACGAGGTTGGAGTATCACCTTAGAG
331820 ATGATGAGGTTAAAGTATCCCTAAAGATGAAAAATTTAGTGTTTGGGAAA
190 ATGATGAGGTTAAAGTATCCCTAAAGATGAAAAATTTAGTGTTTGGGAAA
* * * * * *
331870 TAAACATGGGGTTAGAGCATCCCCTTAAAAATGATGGGGTTAGAGTATCCTCTGAGATGAAAACT
1 TAAAAATGGGGTTAGAGTATCCCCTTAAAAATGGTGGGGTTGGAGTATCCCCTAAGATGAAAA-T
* ** * * * * * *
331935 TTAGTGTTTTAAAAGTAAAAATGGGGATGGAGTATCCTC-CGAGAGATGGTGGGGTTGGAGAATC
65 TTAGTGTTTTAGAAGTAAAAACAGGGTTGGAATATCCCCTCG-GAGATGATGGGGTTGAAGTATC
*
331999 CCC-TAGATGAAAAATT
129 CCCAAAGATGAAAAATT
332015 CAATGTTTTT
Statistics
Matches: 327, Mismatches: 46, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
238 1 0.00
239 22 0.07
240 297 0.91
241 7 0.02
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (239 bp):
TAAAAATGGGGTTAGAGTATCCCCTTAAAAATGGTGGGGTTGGAGTATCCCCTAAGATGAAAATT
TAGTGTTTTAGAAGTAAAAACAGGGTTGGAATATCCCCTCGGAGATGATGGGGTTGAAGTATCCC
CAAAGATGAAAAATTTAGTGTTTGAGAAAGAAAAACGAGGTTGGAGTATCACCTTAGAGATGATG
AGGTTAAAGTATCCCTAAAGATGAAAAATTTAGTGTTTGGGAAA
Found at i:335377 original size:32 final size:33
Alignment explanation
Indices: 335335--335396 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
335325 CAATTTAGTG
*
335335 TGTATCGATACCAAG-AACATGTATTGATAAAA
1 TGTATCGATACCAAGCAACATGTATCGATAAAA
* * *
335367 TGTATTGATACTAAGCAATATGTATCGATA
1 TGTATCGATACCAAGCAACATGTATCGATA
335397 CATTTTGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATGTATCGATAAAA
Found at i:336839 original size:28 final size:28
Alignment explanation
Indices: 336799--336857 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
336789 CAATCTTAGC
336799 CATAGTTTTAAATCCTAGGTAGTGAGGT
1 CATAGTTTTAAATCCTAGGTAGTGAGGT
336827 CATAGTTTTAAATCCTAGGTAGTGAGGT
1 CATAGTTTTAAATCCTAGGTAGTGAGGT
336855 CAT
1 CAT
336858 GAAATGGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (28 bp):
CATAGTTTTAAATCCTAGGTAGTGAGGT
Found at i:342649 original size:3 final size:3
Alignment explanation
Indices: 342641--342674 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
342631 TAAGTCAACT
* *
342641 TCA TCA TCA TTA TCA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
342675 TGATGGTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:343839 original size:23 final size:23
Alignment explanation
Indices: 343812--343856 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
343802 ACTTCTCAAT
343812 TTCTTCAAGA-ATTATAACCCAAA
1 TTCTT-AAGAGATTATAACCCAAA
343835 TTCTTAAGAGATTATAACCCAA
1 TTCTTAAGAGATTATAACCCAA
343857 GGTTGAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (23 bp):
TTCTTAAGAGATTATAACCCAAA
Found at i:344519 original size:22 final size:22
Alignment explanation
Indices: 344487--344529 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
344477 ACTTTGGATT
344487 ATTTTTACTTG-AAAACATTTG
1 ATTTTTACTTGAAAAACATTTG
344508 ATTTATTACTTGAAAAACATTT
1 ATTT-TTACTTGAAAAACATTT
344530 ATACTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTTTTACTTGAAAAACATTTG
Found at i:344801 original size:64 final size:64
Alignment explanation
Indices: 344700--344841 Score: 187
Period size: 64 Copynumber: 2.2 Consensus size: 64
344690 CAAAAACCCA
* * * * *
344700 GAATGTATCGATACAATGAAAAATGTATTGATACATTTTTTTTCCAGAACGTAAGATTTGCCTT
1 GAATGTATCGATACAAAGAAAAATGTATCGATACATTTTCTTTACAGAACGCAAGATTTGCCTT
* * * *
344764 GAATGTATCGATAGAAAGAAAAATTTATCGATACATTTTCTTTATAGAATGCAAGATTTGCCTT
1 GAATGTATCGATACAAAGAAAAATGTATCGATACATTTTCTTTACAGAACGCAAGATTTGCCTT
*
344828 G-ATATATCGATACA
1 GAATGTATCGATACA
344842 TTTCAAGCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 11 0.16
64 56 0.84
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (64 bp):
GAATGTATCGATACAAAGAAAAATGTATCGATACATTTTCTTTACAGAACGCAAGATTTGCCTT
Found at i:347349 original size:51 final size:52
Alignment explanation
Indices: 347292--347413 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 52
347282 CAACTCTCCG
* * *
347292 CAATCGGGGATATTCCAACTCCAATTTTATTTTC-AAAACACCAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAACACAAATTTTTC-A
* *
347343 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACAAATTTTTCA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAACACAAATTTTTCA
347395 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
347414 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 30 0.48
52 28 0.44
53 5 0.08
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAACACAAATTTTTCA
Found at i:347404 original size:52 final size:51
Alignment explanation
Indices: 347292--347413 Score: 174
Period size: 52 Copynumber: 2.4 Consensus size: 51
347282 CAACTCTCCG
* * *
347292 CAATCGGGGATATTCCAACTCCAATTTTATTTTCAAAACACCAATTTTCTA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACACAAATTTTCTA
* *
347343 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACAAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCC-AAAACACAAATTTTCT-A
347395 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
347414 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 31 0.49
52 32 0.51
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACACAAATTTTCTA
Found at i:347457 original size:27 final size:27
Alignment explanation
Indices: 347400--347470 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
347390 TTTCACAATC
347400 GGGGATACTCCAACCCCGTTAATCATCA
1 GGGGATACTCCAACCCCGTTAATCA-CA
**
347428 -GGGATACTCCAACCCCGTTTTTTC-CAA
1 GGGGATACTCCAACCCCG-TTAATCAC-A
347455 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
347471 TGGCTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 1 0.03
27 18 0.47
28 19 0.50
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCACA
Found at i:347508 original size:76 final size:77
Alignment explanation
Indices: 347428--347678 Score: 276
Period size: 79 Copynumber: 3.2 Consensus size: 77
347418 TTAATCATCA
*
347428 GGGATACTCCAACCCCGTTTTTTCCAAGGGGATACTCCAACCCTGGCTTTATTTCTAAAACATCA
1 GGGATACTCCAACCCCGTTTTTTCCAAGGGGATACTCCAACCCTGGTTTTATTTCTAAAACATCA
347493 ATTTTTC-ATCG
66 ATTTTTCAATCG
* * ** *
347504 GGGATACTCTAGCCCCGTTATTTT-TGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGATACTCCAACCCCGTT-TTTTCCAAGGGGATACTCCAACCCTGGTTTTATTTCTAAAACATC
347568 AATTTTTCATAATCG
65 AATTTTTC--AATCG
* ** * * * *
347583 GGAATACTTTAATCCCGTTATTTCCAAGGGGATACTCCAACCCCT-ATTTTATTTTTAAAACA-C
1 GGGATACTCCAACCCCGTTTTTTCCAAGGGGATACTCCAA-CCCTGGTTTTATTTCTAAAACATC
**
347646 TAATTCTCCACAATCG
65 -AATT-T-TTCAATCG
347662 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
347679 GCTTTATTTC
Statistics
Matches: 144, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
76 61 0.42
77 4 0.03
78 4 0.03
79 70 0.49
80 4 0.03
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (77 bp):
GGGATACTCCAACCCCGTTTTTTCCAAGGGGATACTCCAACCCTGGTTTTATTTCTAAAACATCA
ATTTTTCAATCG
Found at i:347622 original size:79 final size:76
Alignment explanation
Indices: 347422--347644 Score: 277
Period size: 76 Copynumber: 2.9 Consensus size: 76
347412 ACCCCGTTAA
* * * *
347422 TCATCAGGG-ATACTCCAACCCCGTTTTTTCCAAGGGGATACTCCAACCCTGGCTTTATTTCTAA
1 TCATC-GGGAATACTCTAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAA
347486 AACATCAATTTT
65 AACATCAATTTT
* * ***
347498 TCATCGGGGATACTCTAGCCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAA
1 TCATCGGGAATACTCTAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAA
347563 ACATCAATTTT
66 ACATCAATTTT
* * ** *
347574 TCATAATCGGGAATACTTTAATCCCGTTATTTCCAAGGGGATACTCCAACCCCTATTTTATTTTT
1 TC---ATCGGGAATACTCTAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCT
347639 AAAACA
63 AAAACA
347645 CTAATTCTCC
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
75 3 0.02
76 66 0.53
79 56 0.45
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (76 bp):
TCATCGGGAATACTCTAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAA
ACATCAATTTT
Found at i:347670 original size:51 final size:51
Alignment explanation
Indices: 347610--347721 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 51
347600 TTATTTCCAA
* * **
347610 GGGGATACTCCAACCCCTATTTTATTTTTAAAACACTAA-TTCTCCACAATC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCT-CACAATC
* * * *
347661 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATC
347712 GGGGATACTC
1 GGGGATACTC
347722 TAGCCCCGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 48 0.92
52 4 0.08
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATC
Found at i:353036 original size:9 final size:8
Alignment explanation
Indices: 353024--353098 Score: 55
Period size: 9 Copynumber: 8.9 Consensus size: 8
353014 CAAAAGGCAA
353024 AAAAAATAG
1 AAAAAA-AG
353033 AAAAAAAG
1 AAAAAAAG
353041 AAAACAACAAG
1 -AAA-AA-AAG
*
353052 AAAAAAACT
1 AAAAAAA-G
353061 AAAAAAA-
1 AAAAAAAG
353068 AAAACAAAG
1 AAAA-AAAG
353077 AAAAAAA-
1 AAAAAAAG
* *
353084 ACAAAAAC
1 AAAAAAAG
353092 AAAAAAA
1 AAAAAAA
353099 AGAGGAAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
7 10 0.18
8 16 0.29
9 22 0.39
10 5 0.09
11 3 0.05
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:353057 original size:13 final size:13
Alignment explanation
Indices: 353033--353101 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 13
353023 AAAAAAATAG
353033 AAAA-AAAG-AAA
1 AAAACAAAGAAAA
*
353044 ACAAC-AAG-AAA
1 AAAACAAAGAAAA
353055 AAAACTAAA-AAAA
1 AAAAC-AAAGAAAA
353068 AAAACAAAGAAAA
1 AAAACAAAGAAAA
*
353081 AAAACAAA-AACA
1 AAAACAAAGAAAA
353093 AAAA-AAAGA
1 AAAACAAAGA
353102 GGAAGAAAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
11 16 0.33
12 11 0.22
13 22 0.45
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (13 bp):
AAAACAAAGAAAA
Found at i:353064 original size:27 final size:25
Alignment explanation
Indices: 353033--353101 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
353023 AAAAAAATAG
353033 AAAAAAAGAAAACAACAAGAAAAAAACT
1 AAAAAAA-AAAAC-A-AAGAAAAAAACT
353061 AAAAAAAAAAACAAAGAAAAAAAAC-
1 AAAAAAAAAAACAAAG-AAAAAAACT
*
353086 AAAAACAAAAA-AAAGA
1 AAAAAAAAAAACAAAGA
353102 GGAAGAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 1 0.03
24 4 0.10
25 13 0.33
26 9 0.23
27 5 0.13
28 7 0.18
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (25 bp):
AAAAAAAAAAACAAAGAAAAAAACT
Found at i:353073 original size:24 final size:24
Alignment explanation
Indices: 353035--353101 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 24
353025 AAAAATAGAA
*
353035 AAAAAGAAAACAACAAGAAAAAAAC
1 AAAAACAAAA-AACAAGAAAAAAAC
353060 TAAAAA-AAAAAACAAAGAAAAAAAAC
1 -AAAAACAAAAAAC-AAG-AAAAAAAC
353086 AAAAACAAAAAA-AAGA
1 AAAAACAAAAAACAAGA
353102 GGAAGAAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 6 0.16
25 12 0.32
26 19 0.50
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (24 bp):
AAAAACAAAAAACAAGAAAAAAAC
Found at i:353080 original size:15 final size:15
Alignment explanation
Indices: 353041--353099 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
353031 AGAAAAAAAG
* *
353041 AAAACAACAAGAA-A
1 AAAACAAAAAAAACA
*
353055 AAAACTAAAAAAAAAA
1 AAAAC-AAAAAAAACA
*
353071 ACAAAGAAAAAAAACA
1 A-AAACAAAAAAAACA
353087 AAAACAAAAAAAA
1 AAAACAAAAAAAA
353100 GAGGAAGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.14
15 17 0.46
16 12 0.32
17 3 0.08
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (15 bp):
AAAACAAAAAAAACA
Found at i:353085 original size:40 final size:40
Alignment explanation
Indices: 353022--353098 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
353012 CTCAAAAGGC
* * * *
353022 AAAAAAAATAGAAAAAAAGAAAACAACAAGAAAAAAACTA
1 AAAAAAAAAACAAAAAAAGAAAACAAAAACAAAAAAACTA
353062 AAAAAAAAAACAAAGAAAA-AAAACAAAAACAAAAAAA
1 AAAAAAAAAACAAA-AAAAGAAAACAAAAACAAAAAAA
353099 AGAGGAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (40 bp):
AAAAAAAAAACAAAAAAAGAAAACAAAAACAAAAAAACTA
Found at i:354518 original size:27 final size:28
Alignment explanation
Indices: 354438--354518 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
354428 AAATCCTTTC
* * *
354438 TCAAAGCCCACTAGTTAGTGGCACCTCT
1 TCAAAGTCCACAAGTCAGTGGCACCTCT
* * * *
354466 TCGAAGTTCGCAAGTCAGTGGCACCTTT
1 TCAAAGTCCACAAGTCAGTGGCACCTCT
354494 TCAAAGTCCACAA-TCAGTGGCACCT
1 TCAAAGTCCACAAGTCAGTGGCACCT
354519 ACTGTATATA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
27 12 0.28
28 31 0.72
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.25
Consensus pattern (28 bp):
TCAAAGTCCACAAGTCAGTGGCACCTCT
Found at i:354808 original size:32 final size:32
Alignment explanation
Indices: 354700--354916 Score: 233
Period size: 32 Copynumber: 6.7 Consensus size: 32
354690 AACCTTTCTC
* *
354700 AAAGCCCACAAAAAGCTGGTGGCAACCTTTTTTC-
1 AAAGCCCAC-ACAAGCTGGTGGCAACC--TCTTCA
* * *
354734 AAAGCCCAGACAAGCTGGTGGCAACCTTTTTCC
1 AAAGCCCACACAAGCTGGTGGCAACC-TCTTCA
354767 AAAGCCCACACAAGCTGGTGGCAACCTCTTCA
1 AAAGCCCACACAAGCTGGTGGCAACCTCTTCA
* * *
354799 AAAGCCCACACAAGTTAGTGGCAA-CTCTTTCT
1 AAAGCCCACACAAGCTGGTGGCAACCTC-TTCA
354831 AAAGCCCACACAAGCTGGTGGCAACCTCTTCA
1 AAAGCCCACACAAGCTGGTGGCAACCTCTTCA
* * * *
354863 AAAGCCCACACAAG-TCAGTGACAACCGCCTCA
1 AAAGCCCACACAAGCT-GGTGGCAACCTCTTCA
* *
354895 AAAGCCTACACAAGTTGGTGGC
1 AAAGCCCACACAAGCTGGTGGC
354917 GTCTCCTTTT
Statistics
Matches: 160, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
31 4 0.03
32 103 0.64
33 45 0.28
34 8 0.05
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (32 bp):
AAAGCCCACACAAGCTGGTGGCAACCTCTTCA
Found at i:354845 original size:64 final size:64
Alignment explanation
Indices: 354693--354887 Score: 257
Period size: 64 Copynumber: 3.0 Consensus size: 64
354683 GTAGAGAAAC
* * * * *
354693 CTTTCTCAAAGCCCACAAAAAGCTGGTGGCAACCTTTTTTC-AAAGCCCAGACAAGCTGGTGGCA
1 CTTTCT-AAAGCCCAC-ACAAGCTGGTGGCAACC--TCTTCAAAAGCCCACACAAGTTAGTGGCA
354757 ACCT
62 A-CT
* *
354761 TTTTCCAAAGCCCACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTTAGTGGCAACT
1 CTTTCTAAAGCCCACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTTAGTGGCAACT
* *
354825 CTTTCTAAAGCCCACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGACAAC
1 CTTTCTAAAGCCCACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTTAGTGGCAAC
354888 CGCCTCAAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
64 65 0.57
65 21 0.18
66 16 0.14
67 9 0.08
68 4 0.03
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (64 bp):
CTTTCTAAAGCCCACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTTAGTGGCAACT
Found at i:354898 original size:96 final size:96
Alignment explanation
Indices: 354730--354916 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
354720 GGCAACCTTT
* * * * * *
354730 TTTCAAAGCCCAGACAAGCTGGTGGCAACCTTTTTCCAAAGCCCACACAAGCTGGTGGCAACCTC
1 TTTCAAAGCCCACACAAGCTGGTGGCAACCTTCTTCAAAAGCCCACACAAGCTAGTGACAACCGC
*
354795 TTCAAAAGCCCACACAAGTTAGTGGCAACTC
66 CTCAAAAGCCCACACAAGTTAGTGGCAACTC
354826 TTTCTAAAGCCCACACAAGCTGGTGGCAACC-TCTTCAAAAGCCCACACAAG-TCAGTGACAACC
1 TTTC-AAAGCCCACACAAGCTGGTGGCAACCTTCTTCAAAAGCCCACACAAGCT-AGTGACAACC
* *
354889 GCCTCAAAAGCCTACACAAGTTGGTGGC
64 GCCTCAAAAGCCCACACAAGTTAGTGGC
354917 GTCTCCTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 1 0.01
96 54 0.68
97 25 0.31
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (96 bp):
TTTCAAAGCCCACACAAGCTGGTGGCAACCTTCTTCAAAAGCCCACACAAGCTAGTGACAACCGC
CTCAAAAGCCCACACAAGTTAGTGGCAACTC
Found at i:355056 original size:52 final size:52
Alignment explanation
Indices: 354977--355230 Score: 244
Period size: 52 Copynumber: 4.9 Consensus size: 52
354967 TGTCACACCA
* * ** *
354977 TTTCTTTATTAAGTCCAATGTTGCTGGCATTGAATCAGCACATTGGTACCTT
1 TTTCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTT
* *
355029 TTTCTTTCTTAAATCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTT
1 TTTCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTT
* * *
355081 TTTCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGTATATTGGTGCCTT
1 TTTCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTT
* ** * * * * * *
355133 TGTC-AACTTTAAGTCTAATGTCGCTAGCCTTGAATCAACACATTGGCACCTT
1 TTTCTTTC-TTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTT
* * * * *
355185 TGTC-ATCTTTAAG-CCTAATATCGCTGGCCTTGAATCAACATATTGG
1 TTTCTTTC-TTAAGTCC-AATATCACTGGCCTTGAATCAGCACATTGG
355231 CATTTTTATC
Statistics
Matches: 171, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
51 2 0.01
52 169 0.99
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (52 bp):
TTTCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTGGTACCTT
Found at i:355114 original size:104 final size:104
Alignment explanation
Indices: 354977--355230 Score: 280
Period size: 104 Copynumber: 2.4 Consensus size: 104
354967 TGTCACACCA
* * * * * * **
354977 TTTCTTTATTAAGTCCAATGTTGCTGGCATTGAATCAGCACATTGGTACCTTTTTC-TTTCTTAA
1 TTTCTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCAACT-TTAA
* *
355041 ATCCAATATCACTGGCCTTGAATCAGCACATTGGCACCTT
65 ATCCAATATCACTAGCCTTGAATCAACACATTGGCACCTT
* * * *
355081 TTTCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGTATATTGGTGCCTTTGTCAACTTTAAG
1 TTTCTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCAACTTTAAA
* * *
355146 TCTAATGTCGCTAGCCTTGAATCAACACATTGGCACCTT
66 TCCAATATCACTAGCCTTGAATCAACACATTGGCACCTT
* * *
355185 TGTC-ATCTTTAAG-CCTAATATCGCTGGCCTTGAATCAACATATTGG
1 TTTCTTTC-TTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGG
355231 CATTTTTATC
Statistics
Matches: 125, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
103 4 0.03
104 120 0.96
105 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (104 bp):
TTTCTTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCAACTTTAAA
TCCAATATCACTAGCCTTGAATCAACACATTGGCACCTT
Found at i:355282 original size:61 final size:61
Alignment explanation
Indices: 355187--355313 Score: 173
Period size: 61 Copynumber: 2.1 Consensus size: 61
355177 GGCACCTTTG
* * * **
355187 TCATCTTTAAGCCTAATATCGCTGGCCTTGAATCAACATATTGGCATTTTTATCATTATTC
1 TCATCTTCAAGCCTAATATCACTGGCCGTGAATCAACATATTGGCACCTTTATCATTATTC
* * *
355248 TCATCTTCAAGCCTGATATCACTTGCCGTGAATCAACATATTGGCACCTTTATCATTCTTC
1 TCATCTTCAAGCCTAATATCACTGGCCGTGAATCAACATATTGGCACCTTTATCATTATTC
*
355309 GCATC
1 TCATC
355314 CTTAAGTCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (61 bp):
TCATCTTCAAGCCTAATATCACTGGCCGTGAATCAACATATTGGCACCTTTATCATTATTC
Found at i:355341 original size:61 final size:59
Alignment explanation
Indices: 355188--355368 Score: 168
Period size: 61 Copynumber: 3.0 Consensus size: 59
355178 GCACCTTTGT
* * * *
355188 CATCTTTAAGCCTAATATCGCTGGCCTTGAATCAACATATTGGCATTTTTATCATTATTCT
1 CATCCTTAAGCCTAATATCGCT-GCCTTGAATCAACATATTGGCA-CTTTATCATTCTTCG
* * *
355249 CAT-CTTCAAGCCTGATATCACTTGCCGTGAATCAACATATTGGCACCTTTATCATTCTTCG
1 CATCCTT-AAGCCTAATATCGC-TGCCTTGAATCAACATATTGGCA-CTTTATCATTCTTCG
* * * * *
355310 CATCCTTAAGTCC-AATGTCGCTGACCTTGAATTAGCATATTGACACTCTTCTCATTCTT
1 CATCCTTAAG-CCTAATATCGCTG-CCTTGAATCAACATATTGGCACT-TTATCATTCTT
355369 ATATCATCTT
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
60 6 0.06
61 86 0.88
62 6 0.06
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (59 bp):
CATCCTTAAGCCTAATATCGCTGCCTTGAATCAACATATTGGCACTTTATCATTCTTCG
Found at i:361494 original size:148 final size:148
Alignment explanation
Indices: 361200--361493 Score: 329
Period size: 148 Copynumber: 2.0 Consensus size: 148
361190 TTAAAAGGAT
* * * *
361200 AAAAACAAACCTACTCCTAATTTATACCTTCGATGTTGAAGCAGACCCGGTAGTTTTATAAGACT
1 AAAAACAAACCTACTCCTAATTCATACCTTCGACGTAGAAGCAGACCCGATAGTTTTATAAGACT
* * * * * * * **
361265 AGGTCTCGAGAGAATGTTAAAATATCTTTAAGATTTTCCATTGACTTAGAAGTGCCTGGTGATCC
66 AAGTCTCGAGAAAATGCTAAAATATCTCTAAGATTTACCATCGACTTAAAAGTGCCCAGTGATCC
*
361330 TAAAGGACTTGAAAAAGC
131 TAAAGGACTCGAAAAAGC
* * * * *
361348 AAAAGCAAACCTACTCCTAATTCGTACCTTCGGCGTAGAAGCCGACCCGATAGTTTTATAGGACT
1 AAAAACAAACCTACTCCTAATTCATACCTTCGACGTAGAAGCAGACCCGATAGTTTTATAAGACT
* * ** *
361413 AAGTTTCGGGGAAAATGCTAGCATAT-TCCTAAGGTTTACCATCGACTTAAAAGTGCCCAGTGAT
66 AAGTCTC-GAGAAAATGCTAAAATATCT-CTAAGATTTACCATCGACTTAAAAGTGCCCAGTGAT
* *
361477 CTTAAGGGACTCGAAAA
129 CCTAAAGGACTCGAAAA
361494 GAGTGCAAAA
Statistics
Matches: 118, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
148 62 0.53
149 56 0.47
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (148 bp):
AAAAACAAACCTACTCCTAATTCATACCTTCGACGTAGAAGCAGACCCGATAGTTTTATAAGACT
AAGTCTCGAGAAAATGCTAAAATATCTCTAAGATTTACCATCGACTTAAAAGTGCCCAGTGATCC
TAAAGGACTCGAAAAAGC
Found at i:363069 original size:11 final size:11
Alignment explanation
Indices: 363055--363105 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
363045 CATCGTTTTC
363055 ATTTTTTTATT
1 ATTTTTTTATT
* *
363066 ATTTTATTATG
1 ATTTTTTTATT
363077 ATTTTTTTATT
1 ATTTTTTTATT
363088 -TTTCTTTGTCATT
1 ATTT-TTT-T-ATT
363101 ATTTT
1 ATTTT
363106 GATTTGATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.09
11 21 0.66
12 1 0.03
13 4 0.12
14 3 0.09
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:365386 original size:21 final size:20
Alignment explanation
Indices: 365314--365409 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
365304 TATATTGATA
* *
365314 CAATGTATCGATACATAAGT
1 CAATGTATCGATACATTACT
**
365334 -TTTGTATCGATACATTTA-T
1 CAATGTATCGATACA-TTACT
*
365353 CATTGTATCGATACATTACT
1 CAATGTATCGATACATTACT
* *
365373 CAGATGTATTGATACATTATT
1 CA-ATGTATCGATACATTACT
365394 CAATGTATCGATACAT
1 CAATGTATCGATACAT
365410 GCAGGCAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.25
20 31 0.48
21 17 0.27
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
CAATGTATCGATACATTACT
Found at i:367324 original size:78 final size:78
Alignment explanation
Indices: 367215--367492 Score: 267
Period size: 79 Copynumber: 3.5 Consensus size: 78
367205 TAATTATAGG
* * *
367215 AAATCGATGTTTTGAGAATAAAATTC-AGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGT
1 AAATCGATGTTTTGAAAATAAAA-CCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGT
367279 AT-CCCGATTGTGGA
65 ATCCCCGATTGT-GA
* * *
367293 AAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAACAACG-GGATTAGAGT
1 AAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGG-TTGGAGT
* *
367357 ATCCCCGATTATAAA
65 ATCCCCGATTGT-GA
* * *** * * *
367372 AAATTGATGCTTT-AGAAATAGGGCCGGGGTTGGAGTATCCACGCAAAAATAACAAGGTTGGAGT
1 AAATCGATGTTTTGA-AAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGT
367436 ATCCCCGATTGTGA
65 ATCCCCGATTGTGA
** * * * * *
367450 GAAATTAATATTTTGCAAATAAAATCGGAGTTGGAATATCCCC
1 -AAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCC
367493 AATTGTGAAA
Statistics
Matches: 160, Mismatches: 33, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
77 3 0.02
78 57 0.36
79 98 0.61
80 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (78 bp):
AAATCGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTA
TCCCCGATTGTGA
Found at i:367541 original size:51 final size:50
Alignment explanation
Indices: 367427--367543 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 50
367417 AAAATAACAA
* * *
367427 GGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTGCAAATAAAATCG
1 GGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTGCAAATAAAACCG
* **
367477 GAGTTGGAATATCCCCAATTGTGAAAAATTGGTATTTTAG-AAATAAAACCG
1 G-GTTGGAGTATCCCCAATTGTGAAAAATTAATATTTT-GCAAATAAAACCG
*
367528 TGGTTAGAGTATCCCC
1 -GGTTGGAGTATCCCC
367544 TCAAAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.02
51 53 0.95
52 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCAATTGTGAAAAATTAATATTTTGCAAATAAAACCG
Found at i:367697 original size:29 final size:28
Alignment explanation
Indices: 367634--367707 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
367624 GATATAAAGC
*
367634 CGGGGTTGGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCATCAAAAATAA
*
367662 CGGGGTTGGAGTATCCTCGATGAAAAA-AA
1 CGGGGTTGGAGTATCC-C-ATCAAAAATAA
*
367691 CGGGGTTCGAGTATCCC
1 CGGGGTTGGAGTATCCC
367708 TAATCATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 17 0.41
29 18 0.44
30 6 0.15
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCATCAAAAATAA
Found at i:367739 original size:108 final size:107
Alignment explanation
Indices: 367489--367759 Score: 292
Period size: 108 Copynumber: 2.5 Consensus size: 107
367479 GTTGGAATAT
** *
367489 CCCCAATTGTGAAAAATTGGTATTTTAGAAATAAAACCGTGGTTAGAGTATCCCCTCAAAAATAA
1 CCCCAATCATGAAAAATTGGTATTTTAGAAATAAAACCGGGGTTAGAGTATCCCCTCAAAAATAA
* *
367554 CGGGATTAGAGTATTCCTGATGAAATAACGGGGTTGGAGTAC
66 CGGGATTAGAGTATTCCTGATGAAAAAACGGGGTTCGAGTAC
** * * ** * * *
367596 CCCCGGTTATGAAAAAATCATATTTTTAGATATAAAGCCGGGGTTGGAGTATCCCCTCAAAAATA
1 CCCCAATCATGAAAAATTGGTA-TTTTAGAAATAAAACCGGGGTTAGAGTATCCCCTCAAAAATA
* * *
367661 ACGGGGTTGGAGTA-TCCTCGATGAAAAAAACGGGGTTCGAGTAT
65 ACGGGATTAGAGTATTCCT-GATG-AAAAAACGGGGTTCGAGTAC
* * * ** * *
367705 CCCTAATCATGAAAAATTGGTGTTTTGGAAATAAATTCGGAGTTTGAGTATCCCC
1 CCCCAATCATGAAAAATTGGTATTTTAGAAATAAAACCGGGGTTAGAGTATCCCC
367760 AATTGCGGTA
Statistics
Matches: 132, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
107 20 0.15
108 81 0.61
109 31 0.23
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (107 bp):
CCCCAATCATGAAAAATTGGTATTTTAGAAATAAAACCGGGGTTAGAGTATCCCCTCAAAAATAA
CGGGATTAGAGTATTCCTGATGAAAAAACGGGGTTCGAGTAC
Found at i:369390 original size:181 final size:182
Alignment explanation
Indices: 369084--369456 Score: 676
Period size: 181 Copynumber: 2.0 Consensus size: 182
369074 GAGCAAATGC
*
369084 ATGGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAAAAACATTTTTATTTCATGGAAC
1 ATGGTGATGGCAAGATATCATCAAGATAAACATGTT-AAAAAAAAACATTTTTACTTCATGGAAC
* *
369149 CTATCTAGCTATTAATCATGCATGAACATGCTCAAGATGTGTTGAAATGACATCCAAATAAGAGA
65 CTATCAAGCTATTAATCATGCATGAACAAGCTCAAGATGTGTTGAAATGACATCCAAATAAGAGA
*
369214 TGAAGATGTGAATATAGAAGGAATGAATAAAGGATGCAAAAACAGGGCCTGTT
130 TGAAGATGTGAATATAGAAGGAATGAACAAAGGATGCAAAAACAGGGCCTGTT
369267 ATGGTGATGGCAAGATATCATCAAGATAAACATGTT-AAAAAAAACATTTTTACTTCATGGAACC
1 ATGGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAAAACATTTTTACTTCATGGAACC
369331 TATCAAGCTATTAATCATGCATGAACAAGCTCAAGATGTGTTGAAATGACATCCAAATAAGAGAT
66 TATCAAGCTATTAATCATGCATGAACAAGCTCAAGATGTGTTGAAATGACATCCAAATAAGAGAT
* *
369396 GAAGATGTGAATATGGAAGGAATGAACAAAGGATGCAAAAACAGGGGCTGTT
131 GAAGATGTGAATATAGAAGGAATGAACAAAGGATGCAAAAACAGGGCCTGTT
369448 ATGGTGATG
1 ATGGTGATG
369457 AAAATGCAAA
Statistics
Matches: 184, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
181 148 0.80
183 36 0.20
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (182 bp):
ATGGTGATGGCAAGATATCATCAAGATAAACATGTTAAAAAAAAACATTTTTACTTCATGGAACC
TATCAAGCTATTAATCATGCATGAACAAGCTCAAGATGTGTTGAAATGACATCCAAATAAGAGAT
GAAGATGTGAATATAGAAGGAATGAACAAAGGATGCAAAAACAGGGCCTGTT
Found at i:370382 original size:20 final size:19
Alignment explanation
Indices: 370359--370443 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
370349 TGCATTGTAA
370359 AATGTATCGATATAATGAGC
1 AATGTATCGATATAATGA-C
370379 AATGTATCG-----AT-AC
1 AATGTATCGATATAATGAC
370392 AATGTATCGATATAATGAGC
1 AATGTATCGATATAATGA-C
* *
370412 AATGTATCGATACAATGCAA
1 AATGTATCGATATAATG-AC
370432 AATGTATCGATA
1 AATGTATCGATA
370444 CATCTGGGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
15 2 0.04
18 2 0.04
19 1 0.02
20 38 0.69
21 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (19 bp):
AATGTATCGATATAATGAC
Found at i:370401 original size:33 final size:33
Alignment explanation
Indices: 370359--370428 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
370349 TGCATTGTAA
370359 AATGTATCGATATAATGAGCAATGTATCGATAC
1 AATGTATCGATATAATGAGCAATGTATCGATAC
370392 AATGTATCGATATAATGAGCAATGTATCGATAC
1 AATGTATCGATATAATGAGCAATGTATCGATAC
370425 AATG
1 AATG
370429 CAAAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (33 bp):
AATGTATCGATATAATGAGCAATGTATCGATAC
Found at i:370427 original size:13 final size:13
Alignment explanation
Indices: 370378--370408 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
370368 ATATAATGAG
370378 CAATGTATCGATA
1 CAATGTATCGATA
370391 CAATGTATCGATA
1 CAATGTATCGATA
*
370404 TAATG
1 CAATG
370409 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:373319 original size:60 final size:59
Alignment explanation
Indices: 373202--373337 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
373192 TGTGACAAAG
* * * *
373202 ACTTGACTAAGTATAGTTAACCGAATAAACTTTGACTGAATACAATCAAATAGAGGCAG
1 ACTTGACTGAGTACAGTTAACCGAATAAAATTTGACTGAATACAATCAAATAGAGGCAA
* *
373261 ACTTGA-TCGAGTACAGTTAAGCC-AATAAAGATTTGACTGATTACAGTCAAAT-GAAGGCAA
1 ACTTGACT-GAGTACAGTTAA-CCGAATAAA-ATTTGACTGAATACAATCAAATAG-AGGCAA
373321 ACTTGACTGAGTACAGT
1 ACTTGACTGAGTACAGT
373338 CAAGTAAGAG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
58 1 0.02
59 23 0.35
60 41 0.62
61 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (59 bp):
ACTTGACTGAGTACAGTTAACCGAATAAAATTTGACTGAATACAATCAAATAGAGGCAA
Found at i:373461 original size:45 final size:43
Alignment explanation
Indices: 373332--374217 Score: 373
Period size: 45 Copynumber: 19.8 Consensus size: 43
373322 CTTGACTGAG
** * * * *
373332 TACAGTCAAGTAAGAGTGAAAAGAATTTGACTAGGGCAACACCAA
1 TACAGTCAAACAAG-GTGAAAA-AGTTTGACCAAGGCAACACCGA
* * *
373377 TACAGTCAAAC-AGAGTGAAAAGAGTTTGACTAGGGCAACACTGA
1 TACAGTCAAACAAG-GTGAAAA-AGTTTGACCAAGGCAACACCGA
* *
373421 TATAGTCAAACCAAGGTTGGAAAAGTTTGACCAAGGCAACACCGA
1 TACAGTCAAA-CAAGG-TGAAAAAGTTTGACCAAGGCAACACCGA
* * * * * *
373466 CATAGTCAAATGAAGGTTAAAATAGTTTGACC-AGGTTAACACCGG
1 TACAGTCAAA-CAAGGTGAAAA-AGTTTGACCAAGG-CAACACCGA
* *
373511 TACAGCCAAACAATGGTGAATAAAGTTTGACTAAGGCAACACCGA
1 TACAGTCAAACAA-GGTGAA-AAAGTTTGACCAAGGCAACACCGA
* * * ** *
373556 TATAGCCAAATAAAGGTGAAAAAAGTTTGATTAGGGCAACACCGA
1 TACAGTCAAA-CAAGGTG-AAAAAGTTTGACCAAGGCAACACCGA
* * *
373601 TACAGTCAAACAAGGGTGGAAAATGTTTGACCAAGGTAACACCAA
1 TACAGTCAAACAA-GGT-GAAAAAGTTTGACCAAGGCAACACCGA
*
373646 TACAGTCAAACAAGGGTG-AAAAGTGCTTGACCAAGGCAACATCGA
1 TACAGTCAAACAA-GGTGAAAAAGT--TTGACCAAGGCAACACCGA
* ** * * * *
373691 TACAATCAAATGAGCGTAAAAAGAGTTTGACTAGGGCAACACTGA
1 TACAGTCAAACAAG-GTGAAAA-AGTTTGACCAAGGCAACACCGA
** * * * **
373736 TACAGTCAAGTGAAAGTGAAACAATTTTGACCAAGTCAACATTGA
1 TACAGTCAA-ACAAGGTGAAA-AAGTTTGACCAAGGCAACACCGA
* * *
373781 TATAGTCAAACAAGG-GTAAGAAGAGTTTGA-CTAGAGCAACACCAA
1 TACAGTCAAACAAGGTG-AA-AA-AGTTTGACCAAG-GCAACACCGA
* * ** * * **
373826 TATAATCAAACAAAATTAAGAAAGTATGACCATA-TTAACACCGA
1 TACAGTCAAACAAGGTGAA-AAAGTTTGACCA-AGGCAACACCGA
* * ** * *
373870 TACAGTCAAATGAAGGTAAGAAAAGAGTTTGACAAAGTTAAAATCGA
1 TACAGTCAAA-CAAGGT--GAAAA-AGTTTGACCAAGGCAACACCGA
* ** * * *
373917 TATAGTCAAACAAAGGCAAGAAAAGCTTGACCAGGGCAACA-TGAA
1 TACAGTCAAAC-AAGGTGA-AAAAGTTTGACCAAGGCAACACCG-A
* * * *
373962 TACAGTCAAACGAGGGTGAAAAGAG-TT-A-CTAGCGCAACATCAA
1 TACAGTCAAAC-AAGGTGAAAA-AGTTTGACCAAG-GCAACACCGA
* * * * *
374005 TATAGTTAAATAAATGTGAGAAAAGTTTGA-CTAGGTCAACACCGA
1 TACAGTCAAA-CAAGGTGA-AAAAGTTTGACCAAGG-CAACACCGA
* * * ** **
374050 TACAATCAAATAAGGGTGAGAAGAA-TTTGATCGGGGCAACATTGA
1 TACAGTCAAACAA-GGTGA-AA-AAGTTTGACCAAGGCAACACCGA
* * * * *
374095 T--A--CAAACGAAAGTGAGAAAAATTTGACCATGTCAACATCGA
1 TACAGTCAAAC-AAGGTGA-AAAAGTTTGACCAAGGCAACACCGA
* * * *
374136 TATAATCAAACAAAGGTGAAAAGAGTTTGAACAAGGCAACAACGA
1 TACAGTCAAAC-AAGGTGAAAA-AGTTTGACCAAGGCAACACCGA
* *
374181 TACAGTCAAATGAAGGTGAAAAGCGTTTGACCAAGGC
1 TACAGTCAAA-CAAGGTGAAAA-AGTTTGACCAAGGC
374218 TGAACCATCA
Statistics
Matches: 643, Mismatches: 145, Indels: 106
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.00
41 27 0.04
42 4 0.01
43 31 0.05
44 99 0.15
45 412 0.64
46 34 0.05
47 34 0.05
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.19
Consensus pattern (43 bp):
TACAGTCAAACAAGGTGAAAAAGTTTGACCAAGGCAACACCGA
Found at i:373971 original size:136 final size:134
Alignment explanation
Indices: 373728--373972 Score: 294
Period size: 136 Copynumber: 1.8 Consensus size: 134
373718 TGACTAGGGC
* * * * * *
373728 AACACTGATACAGTCAAGTGAAAGTGAAACAATTTTGACCAAGTCAACATTGATATAGTCAAACA
1 AACACCGATACAGTCAAATGAAAGTGAAACAAGTTTGACAAAGTCAAAATCGATATAGTCAAACA
* * * * * *
373793 AGGGTAAGAAGAGTTTGACTAGAGCAACACCAATATAATCAAACAAAATTAAGAAAGTATGACCA
66 AAGGCAAGAAAAGCTTGACCAGAGCAACACCAATACAATCAAACAAAATTAAGAAAGTATGACCA
373858 TATT
131 TATT
* *
373862 AACACCGATACAGTCAAATGAAGGTAAGAAA-AGAGTTTGACAAAGTTAAAATCGATATAGTCAA
1 AACACCGATACAGTCAAATGAAAGT--GAAACA-AGTTTGACAAAGTCAAAATCGATATAGTCAA
* ** *
373926 ACAAAGGCAAGAAAAGCTTGACCAGGGCAACATGAATACAGTCAAAC
63 ACAAAGGCAAGAAAAGCTTGACCAGAGCAACACCAATACAATCAAAC
373973 GAGGGTGAAA
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
134 22 0.24
135 1 0.01
136 67 0.74
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (134 bp):
AACACCGATACAGTCAAATGAAAGTGAAACAAGTTTGACAAAGTCAAAATCGATATAGTCAAACA
AAGGCAAGAAAAGCTTGACCAGAGCAACACCAATACAATCAAACAAAATTAAGAAAGTATGACCA
TATT
Found at i:374183 original size:86 final size:86
Alignment explanation
Indices: 374020--374184 Score: 204
Period size: 86 Copynumber: 1.9 Consensus size: 86
374010 TTAAATAAAT
* * * * * * **
374020 GTGAGAAAAGTTTGACTAGGTCAACACCGATACAATCAAATAAGGGTGAGAAGAATTTGATCGGG
1 GTGAGAAAAATTTGACCAGGTCAACACCGATACAATCAAACAAAGGTGAAAAGAATTTGAACAAG
**
374085 GCAACATTGATACAAACGAAA
66 GCAACAACGATACAAACGAAA
* * * *
374106 GTGAGAAAAATTTGACCATGTCAACATCGATATAATCAAACAAAGGTGAAAAGAGTTTGAACAAG
1 GTGAGAAAAATTTGACCAGGTCAACACCGATACAATCAAACAAAGGTGAAAAGAATTTGAACAAG
374171 GCAACAACGATACA
66 GCAACAACGATACA
374185 GTCAAATGAA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (86 bp):
GTGAGAAAAATTTGACCAGGTCAACACCGATACAATCAAACAAAGGTGAAAAGAATTTGAACAAG
GCAACAACGATACAAACGAAA
Found at i:375037 original size:76 final size:77
Alignment explanation
Indices: 374957--375109 Score: 200
Period size: 77 Copynumber: 2.0 Consensus size: 77
374947 CAACTTAAAA
* * * * * * *
374957 AAGAAGAACATGATTAGGAATATATTGTTTTT-ACAATTTTTATCCACAATCAAAACACACTAAA
1 AAGAAAAACATGATGAAGAATATATTGTTTTTAAAAATTTTTATCAACAACCAAAACAAACTAAA
375021 AATAAGCTGAAG
66 AATAAGCTGAAG
* * * *
375033 AAGAAAAACATGATGAAGACTATGTTGTTTTTAAAAATTTTTATCAACAACCAAAACAAATTGAA
1 AAGAAAAACATGATGAAGAATATATTGTTTTTAAAAATTTTTATCAACAACCAAAACAAACTAAA
375098 AATAAGCTGAAG
66 AATAAGCTGAAG
375110 GGCAGTCAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
76 27 0.42
77 38 0.58
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (77 bp):
AAGAAAAACATGATGAAGAATATATTGTTTTTAAAAATTTTTATCAACAACCAAAACAAACTAAA
AATAAGCTGAAG
Found at i:375654 original size:44 final size:44
Alignment explanation
Indices: 375606--375755 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 44
375596 GTAGATGTGC
*
375606 ATGAAACGATGCAAATGCAAGCATCAATAAAAAAGCAAATGCAT
1 ATGAAATGATGCAAATGCAAGCATCAATAAAAAAGCAAATGCAT
* * * * ***
375650 ATGAAATAATGCAAATACCAATGTCATC--T-AAAATGCACATGTGC
1 ATGAAATGATGCAAAT-GCAA-G-CATCAATAAAAAAGCAAATGCAT
* * ***
375694 ATCAAATGATGCAAATGCAAGTATCAATAAAGTGGCAAATGCAT
1 ATGAAATGATGCAAATGCAAGCATCAATAAAAAAGCAAATGCAT
375738 ATGAAATGATGCAAATGC
1 ATGAAATGATGCAAATGC
375756 CAATGTCATC
Statistics
Matches: 80, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
41 3 0.04
42 1 0.01
43 4 0.05
44 63 0.79
45 4 0.05
46 1 0.01
47 4 0.05
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (44 bp):
ATGAAATGATGCAAATGCAAGCATCAATAAAAAAGCAAATGCAT
Found at i:375766 original size:88 final size:88
Alignment explanation
Indices: 375531--375768 Score: 307
Period size: 88 Copynumber: 2.7 Consensus size: 88
375521 ATTCAATTCC
* * * * * * *
375531 AATGCAAGCATTAGA-AAATAAGAAAATACATATGAAATGATGTAAATGCTAATGTCATCCAAAA
1 AATGCAAGCATCA-ATAAAAAAGCAAATGCATATGAAATGATGCAAATGCCAATGTCATCTAAAA
* * *
375595 TGTAGATGTGCATGAAACGATGCA
65 TGCACATGTGCATCAAACGATGCA
* *
375619 AATGCAAGCATCAATAAAAAAGCAAATGCATATGAAATAATGCAAATACCAATGTCATCTAAAAT
1 AATGCAAGCATCAATAAAAAAGCAAATGCATATGAAATGATGCAAATGCCAATGTCATCTAAAAT
*
375684 GCACATGTGCATCAAATGATGCA
66 GCACATGTGCATCAAACGATGCA
* ***
375707 AATGCAAGTATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATGCCAATGTCATCTAA
1 AATGCAAGCATCAATAAAAAAGCAAATGCATATGAAATGATGCAAATGCCAATGTCATCTAA
375769 TCCCAATTTG
Statistics
Matches: 130, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
87 1 0.01
88 129 0.99
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.23
Consensus pattern (88 bp):
AATGCAAGCATCAATAAAAAAGCAAATGCATATGAAATGATGCAAATGCCAATGTCATCTAAAAT
GCACATGTGCATCAAACGATGCA
Found at i:376184 original size:112 final size:110
Alignment explanation
Indices: 376059--376442 Score: 466
Period size: 112 Copynumber: 3.4 Consensus size: 110
376049 GTGCAAACAT
* * ** * * * *
376059 ATCAAATTGTATAAAATATGAATTTAATTGAAAATCAGATAAATTTGATGTTGTTGGCTCAAGAA
1 ATCAGATTGTATAAAACATGAATTTCTTTGAAAATCAAACAAATTTGATGTTGTTGTCTCAAAAA
*
376124 TTTCAAAACTAGCAGAATACATGCCCCATTTTCCTAGGCACGAATGG
66 TTTCAAAA-TAGAAG-ATACATGCCCCATTTTCCTAGGCACGAATGG
** *
376171 ATCAGATCATATAAAACATGAATTTCTTTGAAAATCAAACAAATTTGGTGTCT-TTGTCTCAAAA
1 ATCAGATTGTATAAAACATGAATTTCTTTGAAAATCAAACAAATTTGATGT-TGTTGTCTCAAAA
* *
376235 ATTTCAAAATTGATAGGATGCATGCCCCATTTTCCTAGGCACGAATGG
65 ATTTCAAAATAGA-A-GATACATGCCCCATTTTCCTAGGCACGAATGG
* * **
376283 ATCA-AGTTGTATAAAACGTAAATTTCTTTGAAAATCAAACAAATTTGATGCCGTTGTCTCAAAA
1 ATCAGA-TTGTATAAAACATGAATTTCTTTGAAAATCAAACAAATTTGATGTTGTTGTCTCAAAA
* * * *
376347 ATTTCAAAATTGATAAGATATATGCCCTATTTTCCTAGCCACGAATGG
65 ATTTCAAAA-T-AGAAGATACATGCCCCATTTTCCTAGGCACGAATGG
* *
376395 ATCAGGTTGTATAAAACGTGAATTTCTTTGAAAATCAAACAAATTTGA
1 ATCAGATTGTATAAAACATGAATTTCTTTGAAAATCAAACAAATTTGA
376443 CGTTCTTTCA
Statistics
Matches: 235, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
111 3 0.01
112 227 0.97
113 4 0.02
114 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (110 bp):
ATCAGATTGTATAAAACATGAATTTCTTTGAAAATCAAACAAATTTGATGTTGTTGTCTCAAAAA
TTTCAAAATAGAAGATACATGCCCCATTTTCCTAGGCACGAATGG
Found at i:377086 original size:25 final size:24
Alignment explanation
Indices: 377032--377105 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 24
377022 ACTATCTGCA
377032 CTCTTTTTTTATTTCATGCTTT-TTTT
1 CTCTTTTTTT-TTTC-T-CTTTCTTTT
377058 -TCTTTTTTTTTTCTCTTTCTCTTT
1 CTCTTTTTTTTTTCTCTTTCT-TTT
*
377082 CTCTTTTTTGTTTTTCTATTTCTT
1 CTC-TTTTT-TTTTTCTCTTTCTT
377106 ATTTAAAGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 4 0.10
23 2 0.05
24 7 0.17
25 11 0.26
26 6 0.14
27 12 0.29
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.76
Consensus pattern (24 bp):
CTCTTTTTTTTTTCTCTTTCTTTT
Found at i:377090 original size:21 final size:21
Alignment explanation
Indices: 377064--377104 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
377054 TTTTTCTTTT
*
377064 TTTTTTCTCTTTCTCTTTCTC
1 TTTTTTCTCTTTCTATTTCTC
* *
377085 TTTTTTGTTTTTCTATTTCT
1 TTTTTTCTCTTTCTATTTCT
377105 TATTTAAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTCTCTTTCTATTTCTC
Found at i:377105 original size:19 final size:18
Alignment explanation
Indices: 377054--377105 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
377044 TTCATGCTTT
377054 TTTTTCTTTT-TTTTTTC
1 TTTTTCTTTTCTTTTTTC
*
377071 TCTTTCTCTTTCTCTTTTTTG
1 T-TTT-TCTTT-TCTTTTTTC
377092 TTTTTCTATTTCTT
1 TTTTTCT-TTTCTT
377106 ATTTAAAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 1 0.03
18 3 0.10
19 12 0.41
20 6 0.21
21 7 0.24
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTTTC
Found at i:378518 original size:52 final size:52
Alignment explanation
Indices: 378432--378571 Score: 149
Period size: 52 Copynumber: 2.7 Consensus size: 52
378422 TCTGGAAAGA
* * *
378432 AAATGTATCGATGCATTTTTTATTGTAT-AGATACATTCTAGGTTTTT-AACCC
1 AAATGTATCGATACATTATTCATTGTATCA-ATACATTCTAGGTTTTTGAA-CC
* * *
378484 AAATGTATCGATACATTATTCATTATATCAATACATTTTGGGTTTTTGAACC
1 AAATGTATCGATACATTATTCATTGTATCAATACATTCTAGGTTTTTGAACC
* * * * *
378536 AAATGTGTCGATATATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTATTCATTGTATCAATACAT
378572 GTAGTCAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
52 71 0.96
53 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTATTCATTGTATCAATACATTCTAGGTTTTTGAACC
Found at i:380879 original size:11 final size:11
Alignment explanation
Indices: 380865--380915 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
380855 CATCATTTTC
380865 ATTTTTTTATT
1 ATTTTTTTATT
* *
380876 ATTTTATTATG
1 ATTTTTTTATT
380887 ATTTTTTTATT
1 ATTTTTTTATT
380898 -TTTCTTTGTCATT
1 ATTT-TTT-T-ATT
380911 ATTTT
1 ATTTT
380916 GATTTTATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.09
11 21 0.66
12 1 0.03
13 4 0.12
14 3 0.09
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (11 bp):
ATTTTTTTATT
Done.