Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 2 of 136
Found at i:267331 original size:15 final size:15
Alignment explanation
Indices: 267291--267327 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
267281 AAAATTTTCT
267291 TTTATAATTATAATA
1 TTTATAATTATAATA
*
267306 TATATAA-TATAA-A
1 TTTATAATTATAATA
267319 TTTATAATT
1 TTTATAATT
267328 TATATGTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTATAATTATAATA
Found at i:268429 original size:40 final size:40
Alignment explanation
Indices: 268385--268468 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
268375 GGATTTTCAT
*
268385 TTGTATTGAATCGAATTAACAGAGATTTAGTTAGGTTTAC
1 TTGTATTGAATCAAATTAACAGAGATTTAGTTAGGTTTAC
* *
268425 TTGTATTGAATCAAATTAACATAGATTTAGTTAGGTTTAT
1 TTGTATTGAATCAAATTAACAGAGATTTAGTTAGGTTTAC
268465 TTGT
1 TTGT
268469 GCTAATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (40 bp):
TTGTATTGAATCAAATTAACAGAGATTTAGTTAGGTTTAC
Found at i:279054 original size:24 final size:24
Alignment explanation
Indices: 279026--279075 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
279016 TTGAGGTTGT
* * * *
279026 TCTTCTACCTTTATATTTGACTTA
1 TCTTCGACCTCTATAATCGACTTA
279050 TCTTCGACCTCTATAATCGACTTA
1 TCTTCGACCTCTATAATCGACTTA
279074 TC
1 TC
279076 GATTGGAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.06, T:0.46
Consensus pattern (24 bp):
TCTTCGACCTCTATAATCGACTTA
Found at i:279195 original size:21 final size:23
Alignment explanation
Indices: 279171--279221 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
279161 TTAATTTAAA
279171 TTTAATTTCG-TTTT-ACTTATT
1 TTTAATTTCGCTTTTCACTTATT
*
279192 TTT-ATTTCGCTTTTCATTTATT
1 TTTAATTTCGCTTTTCACTTATT
*
279214 TTAAATTT
1 TTTAATTT
279222 AAATTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 7 0.28
22 8 0.32
23 4 0.16
ACGTcount: A:0.20, C:0.10, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTAATTTCGCTTTTCACTTATT
Found at i:285630 original size:15 final size:15
Alignment explanation
Indices: 285610--285642 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
285600 CTAAGTCTTG
285610 ATACATACCTATTGT
1 ATACATACCTATTGT
285625 ATACATACCTATTGT
1 ATACATACCTATTGT
285640 ATA
1 ATA
285643 TTTCCAGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
ATACATACCTATTGT
Found at i:287368 original size:22 final size:21
Alignment explanation
Indices: 287343--287383 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
287333 TACTTGTTTT
287343 AATATTATTAATATCATTATAC
1 AATATTATTAATAT-ATTATAC
*
287365 AATATTATTATTATATTAT
1 AATATTATTAATATATTAT
287384 TATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATTAATATATTATAC
Found at i:287508 original size:14 final size:14
Alignment explanation
Indices: 287489--287518 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
287479 ATTTTAAAAC
287489 ATATACATATATAT
1 ATATACATATATAT
*
287503 ATATACATATCTAT
1 ATATACATATATAT
287517 AT
1 AT
287519 TTTATAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATACATATATAT
Found at i:292009 original size:9 final size:9
Alignment explanation
Indices: 291995--292051 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
291985 AGTTCAGACT
291995 CAAAAAAAA
1 CAAAAAAAA
292004 C--AAAAAA
1 CAAAAAAAA
292011 CAAAAAAAA
1 CAAAAAAAA
292020 TCAAAAAAAA
1 -CAAAAAAAA
*
292030 TAAAAAAAA
1 CAAAAAAAA
* *
292039 TAAAAAAAT
1 CAAAAAAAA
292048 CAAA
1 CAAA
292052 GTAAAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.17
9 26 0.62
10 9 0.21
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:292035 original size:27 final size:26
Alignment explanation
Indices: 291994--292051 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
291984 GAGTTCAGAC
*
291994 TCAAAAAAAACAAAAAACA-AAAAAAA
1 TCAAAAAAAA-AAAAAAAATAAAAAAA
292020 TCAAAAAAAATAAAAAAAATAAAAAAA
1 TCAAAAAAAA-AAAAAAAATAAAAAAA
292047 TCAAA
1 TCAAA
292052 GTAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (26 bp):
TCAAAAAAAAAAAAAAAATAAAAAAA
Found at i:292044 original size:10 final size:9
Alignment explanation
Indices: 291996--292046 Score: 68
Period size: 9 Copynumber: 5.7 Consensus size: 9
291986 GTTCAGACTC
291996 AAAAAAA-A
1 AAAAAAATA
* *
292004 CAAAAAACA
1 AAAAAAATA
292013 AAAAAAATCA
1 AAAAAAAT-A
292023 AAAAAAATA
1 AAAAAAATA
292032 AAAAAAATA
1 AAAAAAATA
292041 AAAAAA
1 AAAAAA
292047 TCAAAGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
8 6 0.16
9 23 0.61
10 9 0.24
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAATA
Found at i:292900 original size:16 final size:14
Alignment explanation
Indices: 292881--292934 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 14
292871 AATATATATA
292881 AAAAAATGAATGAAAG
1 AAAAAATGAA--AAAG
292897 AAAAAATGAAAAATG
1 AAAAAATGAAAAA-G
292912 AAAAAAATGAAAAAG
1 -AAAAAATGAAAAAG
*
292927 TAAAAATG
1 AAAAAATG
292935 GAGAGGCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 23 0.66
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
AAAAAATGAAAAAG
Found at i:294978 original size:43 final size:43
Alignment explanation
Indices: 294918--295150 Score: 138
Period size: 43 Copynumber: 5.3 Consensus size: 43
294908 AAGAAGGTCA
* *
294918 AAGACACAAACCTTGCCTCTC-CGATTGTGATGGAGCTGGTTG
1 AAGACAAAAATCTTGCCTCTCTCGATTGTGATGGAGCTGGTTG
* ** * *
294960 AAGACAAAAGATCTTGCCTTTCT-GTATTGACA-GCGAAGCAGGTCG
1 AAGACAAAA-ATCTTGCCTCTCTCG-ATTGTGATG-G-AGCTGGTTG
* * * *
295005 AAGACACAAACCTT-CCTCTCTCGGGTTGTGATGGAGATGGTTG
1 AAGACAAAAATCTTGCCTCTCTC-GATTGTGATGGAGCTGGTTG
* * * * * *
295048 AAGACAGCATATCTTGCCT-TCTTGAAT-TGACAGCGAAGCTGGTCG
1 AAGACA-AAAATCTTGCCTCTCTCGATTGTGA-TG-G-AGCTGGTTG
* * *
295093 AAGACACAAACCTTGCCTC-CGTCGGTTGTGATGGAGCTGGTTG
1 AAGACAAAAATCTTGCCTCTC-TCGATTGTGATGGAGCTGGTTG
295136 AAGACAAAAAATCTT
1 AAGAC-AAAAATCTT
295151 ACCTTCCTGC
Statistics
Matches: 141, Mismatches: 33, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
42 11 0.08
43 46 0.33
44 44 0.31
45 37 0.26
46 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
AAGACAAAAATCTTGCCTCTCTCGATTGTGATGGAGCTGGTTG
Found at i:295064 original size:88 final size:88
Alignment explanation
Indices: 294885--295198 Score: 418
Period size: 88 Copynumber: 3.6 Consensus size: 88
294875 NNNNNNNNNG
* * * *
294885 CTTGCCTTCCTGCATTGACAGTGAAGAAGGTCAAAGACACAAACCTTGCCTCTC-CGATTGTGAT
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGAT
*
294949 GGAGCTGGTTGAAGACAAAAGAT
66 GGAGCTGGTTGAAGACAAAAAAT
* *
294972 CTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTT-CCTCTCTCGGGTTGTGA
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTC-GGTTGTGA
* ** *
295036 TGGAGATGGTTGAAGACAGCATAT
65 TGGAGCTGGTTGAAGACAAAAAAT
* * *
295060 CTTGCCTTCTTGAATTGACAGCGAAGCTGGTCGAAGACACAAACCTTGCCTC-CGTCGGTTGTGA
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGGTTGTGA
295124 TGGAGCTGGTTGAAGACAAAAAAT
65 TGGAGCTGGTTGAAGACAAAAAAT
* * * * *
295148 CTTACCTTCCTGCATTGACAGCGAATCAGATCGAAGACACAAGCCCTGCCT
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
295199 AAAGATCTTG
Statistics
Matches: 197, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
86 6 0.03
87 43 0.22
88 142 0.72
89 6 0.03
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGAT
GGAGCTGGTTGAAGACAAAAAAT
Found at i:295255 original size:44 final size:43
Alignment explanation
Indices: 295205--295699 Score: 197
Period size: 44 Copynumber: 11.3 Consensus size: 43
295195 GCCTAAAGAT
* *
295205 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACGCAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGCAGGTCGAAGACACAAAC
* * * * * *
295249 CTTGCCTCTCTCT-TTTGTGA-TGG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCT-TC-CTGTAT-TGACAGGAAGCAGGTCGAAGACACAA-AC
295293 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGCAGGTCGAAGACACAAAC
* * * * * *
295337 CTTGCCTCTCTCGGT-TGTGA-TGG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCT-TC-CTGTAT-TGACAGGAAGCAGGTCGAAGACACAA-AC
295381 CTTGCCTTCCTGTATTGACAGTGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGCAGGTCGAAGACACAAAC
* * * * * * *
295425 CTTGCCTCTCTCGGT-TGTGA-TGG-AGCTGGTTGAAGATAACAGAT
1 CTTGCCT-TC-CTGTAT-TGACAGGAAGCAGGTCGAAGA-CACAAAC
* * * * *
295469 CTTGCCTTCCTGTATTAACAGCGAAACAGATTGAAGACACAAGC
1 CTTGCCTTCCTGTATTGACAG-GAAGCAGGTCGAAGACACAAAC
* * * ** * * * * *
295513 CTTACCTCTCTCGGT-TTTAGTGG-AGTAGGTCAAAGATAGCAGAT
1 CTTGCCT-TC-CTGTATTGACAGGAAGCAGGTCGAAGACA-CAAAC
* * * *
295557 CTTGCCTTCCTGCATTGACAGCAAAGTAGATCGAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGCAGGTCGAAGACACAAAC
* * ** * * * *
295601 CTTGCCTCCCTCG-GTTGTATTGG-AGCAGGTCAAAGATAACAGAT
1 CTTGCCTTCCT-GTATTG-ACAGGAAGCAGGTCGAAGA-CACAAAC
** * **
295645 CTTGCCTTCCTGCCTTGACAGCGAAGCAGATTAAAGACACAAAC
1 CTTGCCTTCCTGTATTGACAG-GAAGCAGGTCGAAGACACAAAC
*
295689 CTTACCTTCCT
1 CTTGCCTTCCT
295700 CGGTTGCAGT
Statistics
Matches: 325, Mismatches: 90, Indels: 72
0.67 0.18 0.15
Matches are distributed among these distances:
42 18 0.06
43 80 0.25
44 122 0.38
45 85 0.26
46 20 0.06
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (43 bp):
CTTGCCTTCCTGTATTGACAGGAAGCAGGTCGAAGACACAAAC
Found at i:295255 original size:57 final size:57
Alignment explanation
Indices: 295146--295255 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
295136 AAGACAAAAA
* * *
295146 ATCTTACCTTCCTGCATTGACAGCGAATCAGATCGAAGACACAAGCCCTGCCTAAAG
1 ATCTTACCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCCTGCCTAAAG
* * * * *
295203 ATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACGCAAACCTTGCCT
1 ATCTTACCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCCTGCCT
295256 CTCTCTTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (57 bp):
ATCTTACCTTCCTGCATTGACAGCGAAGCAGATCAAAGACACAAACCCTGCCTAAAG
Found at i:295327 original size:145 final size:145
Alignment explanation
Indices: 295058--295343 Score: 430
Period size: 145 Copynumber: 2.0 Consensus size: 145
295048 AAGACAGCAT
* * *
295058 ATCTTGCCTTCTTGAATTGACAGCGAAGCTGGTCGAAGACACAAACCTTGCCTCCGTCGGTTGTG
1 ATCTTGCCTTCCTGAATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCCGTCGGTTGTG
*
295123 ATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGCATTGACAGCGAATCAGATCGAAGACAC
66 ATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAC
*
295188 AAGCCCTGCCTAAAG
131 AAACCCTGCCTAAAG
* * **
295203 ATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACGCAAACCTTGCCTCTC-TCTTTTGT
1 ATCTTGCCTTCCTGAATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTC-CGTCGGTTGT
* * * *
295267 GATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACA
65 GATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGCATTGACAGCGAAGCAGATCGAAGACA
*
295332 CAAACCTTGCCT
130 CAAACCCTGCCT
295344 CTCTCGGTTG
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
145 125 0.99
146 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (145 bp):
ATCTTGCCTTCCTGAATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCCGTCGGTTGTG
ATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAC
AAACCCTGCCTAAAG
Found at i:295348 original size:88 final size:88
Alignment explanation
Indices: 295199--295705 Score: 644
Period size: 88 Copynumber: 5.8 Consensus size: 88
295189 AGCCCTGCCT
* * * **
295199 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACGCAAACCTTGCCTCTCTCTTT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
*
295264 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGATA
*
295287 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
*
295352 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGATA
* *
295375 AAAGATCTTGCCTTCCTGTATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
295440 TGTGATGGAGCTGGTTGAAGATA
66 TGTGATGGAGCTGGTTGAAGATA
* * * * * *
295463 ACAGATCTTGCCTTCCTGTATTAACAGCGAAACAGATTGAAGACACAAGCCTTACCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
* **
295528 T-TTAGTGGAG-TAGGTCAAAGATA
66 TGTGA-TGGAGCT-GGTTGAAGATA
** * * * *
295551 GCAGATCTTGCCTTCCTGCATTGACAGCAAAGTAGATCGAAGACACAAACCTTGCCTCCCTCGGT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
* **
295616 TGT-ATTGGAGCAGGTCAAAGATA
66 TGTGA-TGGAGCTGGTTGAAGATA
* ** ** *
295639 ACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATTAAAGACACAAACCTTACCT-TCCTCGG
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT-CTCGG
295703 TTG
65 TTG
295706 CAGTGGAACA
Statistics
Matches: 377, Mismatches: 37, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
87 3 0.01
88 373 0.99
89 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
TGTGATGGAGCTGGTTGAAGATA
Found at i:295373 original size:233 final size:233
Alignment explanation
Indices: 294966--295431 Score: 720
Period size: 233 Copynumber: 2.0 Consensus size: 233
294956 GTTGAAGACA
* *
294966 AAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTCCTCTCTCGGGT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACACAAACCTTCCTCTCTCGGGT
** * * *
295031 TGTGATGGAGATGGTTGAAGACAGCATATCTTGCCTTCTTGAATTGACAGCGAAGCTGGTCGAAG
66 TGTGATGGAGATGGTTGAAGACAAAAGATCTTGCCTTCCTGAATTGACAGCGAAGCAGGTCGAAG
295096 ACACAAACCTTGCCTCCGTCGGTTGTGATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGC
131 ACACAAACCTTGCCTCCGTCGGTTGTGATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGC
* *
295161 ATTGACAGCGAATCAGATCGAAGACACAAGCCCTGCCT
196 ATTGACAGCGAAGCAGATCGAAGACACAAACCCTGCCT
* **
295199 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACGCAAACCTTGCCTCTCTC-TT
1 AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACACAAACCTT-CCTCTCTCGGG
* *
295263 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAA
65 TTGTGATGGAGATGGTTGAAGACAAAAGATCTTGCCTTCCTGAATTGACAGCGAAGCAGGTCGAA
* *
295328 GACACAAACCTTGCCTCTC-TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCT
130 GACACAAACCTTGCCTC-CGTCGGTTGTGATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCT
* * * *
295392 GTATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCT
194 GCATTGACAGCGAAGCAGATCGAAGACACAAACCCTGCCT
295432 CTCTCGGTTG
Statistics
Matches: 211, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
233 202 0.96
234 9 0.04
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (233 bp):
AAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACACAAACCTTCCTCTCTCGGGT
TGTGATGGAGATGGTTGAAGACAAAAGATCTTGCCTTCCTGAATTGACAGCGAAGCAGGTCGAAG
ACACAAACCTTGCCTCCGTCGGTTGTGATGGAGCTGGTTGAAGACAAAAAATCTTACCTTCCTGC
ATTGACAGCGAAGCAGATCGAAGACACAAACCCTGCCT
Found at i:295479 original size:321 final size:320
Alignment explanation
Indices: 294885--295513 Score: 1010
Period size: 321 Copynumber: 2.0 Consensus size: 320
294875 NNNNNNNNNG
*
294885 CTTGCCTTCCTGCATTGACAGTGAAGAAGGTCAAAGACACAAACCTTGCCTCTCCGATTGTGATG
1 CTTGCCTTCCTGCATTGACAGCGAAGAAGGTCAAAGACACAAACCTTGCCTCTCCGATTGTGATG
*
294950 GAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA
66 GAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA
** * *
295015 CCTTCCTCTCTCGGGTTGTGATGGAGATGGTTGAAGACAGCATATCTTGCCTTCTTGAATTGACA
131 CCTTCCTCTCTCGGGTTGTGATGGAGATGGTTGAAGACAAAAGATCTTGCCTTCCTGAATTGACA
*
295080 GCGAAGCTGGTCGAAGACACAAACCTTGCCTCCGTCGGTTGTGATGGAGCTGGTTGAAGACAAAA
196 GCGAAGCAGGTCGAAGACACAAACCTTGCCTCCGTCGGTTGTGATGGAGCTGGTTGAAGACAAAA
* *
295145 AATCTTACCTTCCTGCATTGACAGCGAATCAGATCGAAGACACAAGCCCTGCCTAAAGAT
261 AATCTTACCTTCCTGCATTAACAGCGAAACAGATCGAAGACACAAGCCCTGCCTAAAGAT
* * * **
295205 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCAAAGACGCAAACCTTGCCTCTCTCTTTTGTGAT
1 CTTGCCTTCCTGCATTGACAGCGAAGAAGGTCAAAGACACAAACCTTGCCTCTC-CGATTGTGAT
295270 GGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAA
65 GGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAA
* *
295335 ACCTTGCCTCTCTC-GGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGA
130 ACCTT-CCTCTCTCGGGTTGTGATGGAGATGGTTGAAGACAAAAGATCTTGCCTTCCTGAATTGA
* *
295399 CAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGGTTGTGATGGAGCTGGTTGAAGATA
194 CAGCGAAGCAGGTCGAAGACACAAACCTTGCCTC-CGTCGGTTGTGATGGAGCTGGTTGAAGACA
* * * * *
295463 ACAGATCTTGCCTTCCTGTATTAACAGCGAAACAGATTGAAGACACAAGCC
258 AAAAATCTTACCTTCCTGCATTAACAGCGAAACAGATCGAAGACACAAGCC
295514 TTACCTCTCT
Statistics
Matches: 283, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
320 50 0.18
321 224 0.79
322 9 0.03
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (320 bp):
CTTGCCTTCCTGCATTGACAGCGAAGAAGGTCAAAGACACAAACCTTGCCTCTCCGATTGTGATG
GAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA
CCTTCCTCTCTCGGGTTGTGATGGAGATGGTTGAAGACAAAAGATCTTGCCTTCCTGAATTGACA
GCGAAGCAGGTCGAAGACACAAACCTTGCCTCCGTCGGTTGTGATGGAGCTGGTTGAAGACAAAA
AATCTTACCTTCCTGCATTAACAGCGAAACAGATCGAAGACACAAGCCCTGCCTAAAGAT
Found at i:295761 original size:50 final size:50
Alignment explanation
Indices: 295689--296071 Score: 378
Period size: 50 Copynumber: 7.9 Consensus size: 50
295679 AGACACAAAC
* * * *
295689 CTTACCTTCCTCG-GTTGCAGTGGAACAGATTGAAGCTACAACAGCGAAT
1 CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* *
295738 CTTACTTTCCTAGCGTTGCAGTGGAACAGGTTGAAGCTACAACAGCGGAT
1 CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* * ** *
295788 CTTACTTTCCT-GACATTGCAATTAAAAAGATTGAAGCTATAACAGCGGAT
1 CTTACTTTCCTAG-CGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* * *
295838 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGTGGAT
1 CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* * ** *
295888 CTT-GTTTCC--CCG--GCAGTTAAAAAGACTGAAGCTACAACAGCGGAT
1 CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* * * **
295933 CTT-GTTTCC--CCG--ACAGTTAAAAAGATTGAAGCTACAACAGCGGAT
1 CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* *
295978 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGAT
1 CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
* * * * *
296028 CTTACTTCCCTAACATTGCAAT-TATAAAGATTGAAGCTACAACA
1 CTTACTTTCCTAGCGTTGCAGTGGA-AAAGATTGAAGCTACAACA
296072 ATAGATCTTA
Statistics
Matches: 282, Mismatches: 43, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
45 74 0.26
46 5 0.02
47 1 0.00
48 1 0.00
49 18 0.06
50 182 0.65
51 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (50 bp):
CTTACTTTCCTAGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGCGGAT
Found at i:295918 original size:45 final size:45
Alignment explanation
Indices: 295869--295980 Score: 197
Period size: 45 Copynumber: 2.5 Consensus size: 45
295859 TGGAACAGAT
* *
295869 TGAAGCTACAACAGTGGATCTTGTTTCCCCGGCAGTTAAAAAGAC
1 TGAAGCTACAACAGCGGATCTTGTTTCCCCGACAGTTAAAAAGAC
*
295914 TGAAGCTACAACAGCGGATCTTGTTTCCCCGACAGTTAAAAAGAT
1 TGAAGCTACAACAGCGGATCTTGTTTCCCCGACAGTTAAAAAGAC
295959 TGAAGCTACAACAGCGGATCTT
1 TGAAGCTACAACAGCGGATCTT
295981 ACTTTCCTAG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (45 bp):
TGAAGCTACAACAGCGGATCTTGTTTCCCCGACAGTTAAAAAGAC
Found at i:296012 original size:140 final size:145
Alignment explanation
Indices: 295689--296034 Score: 463
Period size: 140 Copynumber: 2.4 Consensus size: 145
295679 AGACACAAAC
* * * *
295689 CTTACCTTCCTCG-GTTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGCG
1 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTTCC-ACCG
* * ** *
295753 TTGCAGTGGAACAGGTTGAAGCTACAACAGCGGATCTTACTTTCCTGACATTGCAATTAAAAAGA
65 -TGCAGTGAAAAAGACTGAAGCTACAACAGCGGATCTTACTTTCCCGACA-TG--ATTAAAAAGA
*
295818 TTGAAGCTATAACAGCGGAT
126 TTGAAGCTACAACAGCGGAT
* *
295838 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGTGGATCTT-GTTTCC-CCG-
1 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTTCCACCGT
* *
295900 GCAGTTAAAAAGACTGAAGCTACAACAGCGGATCTT-GTTTCCCCGACA-G-TTAAAAAGATTGA
66 GCAGTGAAAAAGACTGAAGCTACAACAGCGGATCTTACTTT-CCCGACATGATTAAAAAGATTGA
295962 AGCTACAACAGCGGAT
130 AGCTACAACAGCGGAT
295978 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
1 CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTT
296035 CCCTAACATT
Statistics
Matches: 178, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
140 80 0.45
141 2 0.01
143 1 0.01
144 3 0.02
145 37 0.21
147 2 0.01
149 16 0.09
150 37 0.21
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (145 bp):
CTTACTTTCCTAGTGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTTCCACCGT
GCAGTGAAAAAGACTGAAGCTACAACAGCGGATCTTACTTTCCCGACATGATTAAAAAGATTGAA
GCTACAACAGCGGAT
Found at i:297542 original size:16 final size:16
Alignment explanation
Indices: 297490--297557 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
297480 TTCATTTTTT
297490 TATTTTATTTTATTTA
1 TATTTTATTTTATTTA
* *
297506 T-TTTT-TTAACTATTAA
1 TATTTTATT--TTATTTA
297522 T-TTTTATTTTATTTA
1 TATTTTATTTTATTTA
*
297537 TATTTTCATTTATCTTTA
1 TATTTT-ATTT-TATTTA
297555 TAT
1 TAT
297558 ATATGTGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 15 0.37
17 6 0.15
18 8 0.20
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTATTTTATTTA
Found at i:297615 original size:3 final size:3
Alignment explanation
Indices: 297587--297662 Score: 66
Period size: 3 Copynumber: 25.7 Consensus size: 3
297577 TAATATGTGC
* * * *
297587 TAT TAT T-T T-T TAT TCT TAT ATAT TAT TAT TAA AAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * *
297631 TAT TAT TAT TAG CAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
297663 AATACCTTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:298807 original size:93 final size:94
Alignment explanation
Indices: 298648--298834 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 94
298638 GGACCAAACT
298648 TGTTGTTTTAATAAAATCAAACCGTTTATTAAAAACAACCACATTTTGAGGATATCCAATCACAC
1 TGTTGTTTTAATAAAATCAAACCGTTTATTAAAAACAACCACATTTTGAGGATATCCAATCACAC
298713 CTCATAAAAAAAGATT-GTGGCGACTCCC
66 CTCATAAAAAAAGATTGGTGGCGACTCCC
298741 TGTTGTTTTAATAAAATCAAACCGTTTATTAAAAACAACCACATTTTGAGGATATCCAATCACAC
1 TGTTGTTTTAATAAAATCAAACCGTTTATTAAAAACAACCACATTTTGAGGATATCCAATCACAC
298806 CTCATAAAAAAAGATTGGTGGCGACTCCC
66 CTCATAAAAAAAGATTGGTGGCGACTCCC
298835 GTTTCATTTT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 81 0.87
94 12 0.13
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (94 bp):
TGTTGTTTTAATAAAATCAAACCGTTTATTAAAAACAACCACATTTTGAGGATATCCAATCACAC
CTCATAAAAAAAGATTGGTGGCGACTCCC
Found at i:300862 original size:18 final size:18
Alignment explanation
Indices: 300841--300892 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
300831 CAATAAATAA
300841 ATTAAAAATTATAAAAAT-
1 ATTAAAAA-TATAAAAATC
*
300859 ATTAAAAAAATAAAAAATC
1 ATTAAAAATAT-AAAAATC
*
300878 AATAAAAATATAAAA
1 ATTAAAAATATAAAA
300893 GTTCATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 18 0.62
19 9 0.31
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
ATTAAAAATATAAAAATC
Found at i:302718 original size:109 final size:109
Alignment explanation
Indices: 302514--302789 Score: 425
Period size: 109 Copynumber: 2.6 Consensus size: 109
302504 AAGATTCAAG
*
302514 AGGATATTTGGCTT-TTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCT
1 AGGATATTTGG-TTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCT
* * * * * *
302575 TGAATTTCCAAACGCTAAATATTGCCTTGTTTTGAAATTTTTAAA
65 CGAATTACCAAACACAAAACATTGCCTTATTTTGAAATTTTTAAA
302620 AGGATATTTGGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
1 AGGATATTTGGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
302685 GAATTACCAAACACAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTACCAAACACAAAACATTGCCTTATTTTGAAATTTTTAAA
* * *
302729 AGGATACTTAGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAAGGCACGTTT
1 AGGATATTTGGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTT
302790 TCCCGTAGTT
Statistics
Matches: 156, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
105 2 0.01
106 24 0.15
108 28 0.18
109 102 0.65
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (109 bp):
AGGATATTTGGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
GAATTACCAAACACAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:302817 original size:109 final size:108
Alignment explanation
Indices: 302528--302829 Score: 423
Period size: 109 Copynumber: 2.8 Consensus size: 108
302518 TATTTGGCTT
* *
302528 TTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTTGAATTTCCAAACGC
1 TTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAA-TTCCAAACGC
* * *
302590 TAAATATTGCCTTGTTTTGAAATTTTTAAAAGGATATTTGGTTA
65 TAAATATTGCCTTATTTTGAAATTTTTAAAAGGATACTTAGTTA
*
302634 TTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTACCAAACAC
1 TTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATT-CCAAACGC
* *
302699 AAAACATTGCCTTATTTTGAAATTTTTAAAAGGATACTTAGTTA
65 TAAATATTGCCTTATTTTGAAATTTTTAAAAGGATACTTAGTTA
* * *
302743 TTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAAGGCACGTTTTCC-CGTAGTTCCAAATG
1 TTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACG-TTTCCTCG-AATTCCAAACG
* *
302807 CTAAATATTGCCTCATTTAGAAA
64 CTAAATATTGCCTTATTTTGAAA
302830 AATTTTCCTT
Statistics
Matches: 174, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
106 13 0.07
108 30 0.17
109 123 0.71
110 8 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (108 bp):
TTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTCCAAACGCT
AAATATTGCCTTATTTTGAAATTTTTAAAAGGATACTTAGTTA
Found at i:303115 original size:15 final size:15
Alignment explanation
Indices: 303100--303136 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
303090 TAACAATAAT
303100 ATAAATAATAAAAATA
1 ATAAA-AATAAAAATA
303116 ATAAAAATAAAAATA
1 ATAAAAATAAAAATA
303131 ATAAAA
1 ATAAAA
303137 TTACTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAAAATA
Found at i:303115 original size:18 final size:18
Alignment explanation
Indices: 303071--303137 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
303061 AAGCTATTAT
* *
303071 ATAATAATAATAT-GATA
1 ATAAAAATAATATAAATA
*
303088 AGTAACAATAATATAAATA
1 A-TAAAAATAATATAAATA
303107 ATAAAAAT-A-ATAAA-A
1 ATAAAAATAATATAAATA
303122 ATAAAAATAATA-AAAT
1 ATAAAAATAATATAAAT
303138 TACTGAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 9 0.21
16 9 0.21
17 3 0.07
18 17 0.40
19 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (18 bp):
ATAAAAATAATATAAATA
Found at i:303136 original size:9 final size:9
Alignment explanation
Indices: 303094--303134 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
303084 GATAAGTAAC
*
303094 AATAATATA
1 AATAATAAA
303103 AATAATAAA
1 AATAATAAA
303112 AATAATAAA
1 AATAATAAA
303121 AATAA-AAA
1 AATAATAAA
303129 TAATAA
1 -AATAA
303135 AATTACTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 3 0.10
9 27 0.90
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAATAAA
Found at i:304554 original size:24 final size:24
Alignment explanation
Indices: 304521--304569 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
304511 CCTTTTAAGC
*
304521 TGCTCTACTGCAACTTCAGGGAGA
1 TGCTCCACTGCAACTTCAGGGAGA
304545 TGCTCCACTGCAACTTCAGGGAGA
1 TGCTCCACTGCAACTTCAGGGAGA
304569 T
1 T
304570 AAGATTTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
TGCTCCACTGCAACTTCAGGGAGA
Found at i:304861 original size:89 final size:89
Alignment explanation
Indices: 304759--305187 Score: 678
Period size: 89 Copynumber: 4.8 Consensus size: 89
304749 GCTTCACTGC
* * * * * *
304759 CAGTACAGGAAGGCAAGGCTGGTGTCCTCGATCTGCTTCTCTGCCAGTACAGGAAGGCAAGATCT
1 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
* *
304824 ACTATCTTCAGTCTGCTCCGCTGT
66 ACTATCTTTAGTCTACTCCGCTGT
* * * * *
304848 CAGTACAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCAGTACAAGAAGGCATGATCT
1 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
304913 ACTATCTTTAGTCTACTCCGCTGT
66 ACTATCTTTAGTCTACTCCGCTGT
*
304937 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCT
1 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
*
305002 ACTATCTTTAGTCTGCTCCGCTGT
66 ACTATCTTTAGTCTACTCCGCTGT
*
305026 CAGTACAGGAAGGCAAGACTGGTTTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
1 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
*
305091 GCTATCTTTAGTCTACTCCGCTGT
66 ACTATCTTTAGTCTACTCCGCTGT
* * *
305115 CAGTATAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCT
1 CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
305180 ACTATCTT
66 ACTATCTT
305188 CTTTGATCTG
Statistics
Matches: 317, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 317 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (89 bp):
CAGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATCT
ACTATCTTTAGTCTACTCCGCTGT
Found at i:305176 original size:44 final size:44
Alignment explanation
Indices: 304734--305176 Score: 426
Period size: 44 Copynumber: 10.0 Consensus size: 44
304724 CTGTAAACTA
* * * * *
304734 TGGTGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGGC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAC
* * * *
304778 TGGTGTCCTCGATCTGCTTCTCTGCCAGTACAGGAAGGCAAGATC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-C
** * *
304823 TACTATCTTC-AGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGC
1 TGGTATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGAC
* * * * *
304867 TGGTGTCTTTGATCTGCTTCGCTGCCAGTACAAGAAGGCATGATC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-C
** * * *
304912 TACTATCTT-TAGTCTACTCCGCTGTCAGTACAGGAAGGCAAGAC
1 TGGTATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGAC
* * *
304956 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-C
** * *
305001 TACTATCTT-TAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGAC
1 TGGTATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGAC
* * *
305045 TGGTTTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCATGATC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA-C
* * * * *
305090 TGCTATCTT-TAGTCTACTCCGCTGTCAGTATAGGAAGGCAAGAC
1 TGGTATCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGAC
* *
305134 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGA
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
305177 TCTACTATCT
Statistics
Matches: 322, Mismatches: 65, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
44 181 0.56
45 141 0.44
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.29
Consensus pattern (44 bp):
TGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAC
Found at i:305796 original size:17 final size:17
Alignment explanation
Indices: 305766--305819 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
305756 TGGCCTCTCA
*
305766 TTTTCTCTTTTTTTTTCT
1 TTTTC-CTTCTTTTTTCT
305784 TTTTCCTTCTTTTTTCT
1 TTTTCCTTCTTTTTTCT
305801 TTCTT-CTTCTTTTTT-T
1 TT-TTCCTTCTTTTTTCT
305817 TTT
1 TTT
305820 GAAATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 1 0.03
16 3 0.09
17 23 0.68
18 7 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCCTTCTTTTTTCT
Found at i:306514 original size:42 final size:42
Alignment explanation
Indices: 306455--306534 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
306445 ATAAATTCTG
306455 TTGATTCTTTATAGGGTAGGATCTGTTTTTCATCTTGTCCTA
1 TTGATTCTTTATAGGGTAGGATCTGTTTTTCATCTTGTCCTA
306497 TTGATTCTTTATAGGGTAGGATCTGTTTTTCATCTTGT
1 TTGATTCTTTATAGGGTAGGATCTGTTTTTCATCTTGT
306535 TGTACCATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.51
Consensus pattern (42 bp):
TTGATTCTTTATAGGGTAGGATCTGTTTTTCATCTTGTCCTA
Found at i:310478 original size:109 final size:109
Alignment explanation
Indices: 310175--310478 Score: 488
Period size: 109 Copynumber: 2.8 Consensus size: 109
310165 AAGATTCAAG
*
310175 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
*
310237 GAATTTCCAAACGCTAAATATTGCATTGTTTTGAAATTTTTAAA
66 GAATTTCCAAACGCTAAATATTGCATTATTTTGAAATTTTTAAA
310281 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * * *
310346 GAATTACCAAACGCAAAACATTGCTTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCTAAATATTGCATTATTTTGAAATTTTTAAA
* * *
310390 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACGTTAGTGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* *
310455 GAATTTCCAAATGTTAAATATTGC
66 GAATTTCCAAACGCTAAATATTGC
310479 CTCATTTAGA
Statistics
Matches: 181, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
106 27 0.15
108 28 0.15
109 126 0.70
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
GAATTTCCAAACGCTAAATATTGCATTATTTTGAAATTTTTAAA
Found at i:310648 original size:16 final size:16
Alignment explanation
Indices: 310627--310665 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
310617 TGAATTATAA
*
310627 AAAAATAAAATAAGAT
1 AAAAATAAAATAAAAT
*
310643 AAAAATAACATAAAAT
1 AAAAATAAAATAAAAT
310659 AAAAATA
1 AAAAATA
310666 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:310853 original size:3 final size:3
Alignment explanation
Indices: 310845--310920 Score: 84
Period size: 3 Copynumber: 25.3 Consensus size: 3
310835 AAGCTATTAT
* *
310845 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATG ATA AGTA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* *
310890 ATA TTA CA-A ATA ATA AAA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
310921 AATTACTGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 3 0.05
3 56 0.90
4 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:312784 original size:25 final size:25
Alignment explanation
Indices: 312725--312787 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
312715 CCCGTTAATA
*
312725 GCTCTCATGAG-TATCTCGATATTG
1 GCTCTCATGAGCTTTCTCGATATTG
* *
312749 GCTTTCTTGAGCTTTCT-GATATATG
1 GCTCTCATGAGCTTTCTCGATAT-TG
*
312774 GCTCTCGTGAGCTT
1 GCTCTCATGAGCTT
312788 CCCGTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (25 bp):
GCTCTCATGAGCTTTCTCGATATTG
Found at i:312966 original size:24 final size:25
Alignment explanation
Indices: 312911--312968 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
312901 AAGGCTCTTT
* *
312911 CATGAGCTTCCTGATATATGGCTCT
1 CATGAGCTTCATGATATATGGCTCG
** *
312936 CCGGAGCTTCATGATAT-TGGCTGG
1 CATGAGCTTCATGATATATGGCTCG
312960 CATGAGCTT
1 CATGAGCTT
312969 TCAGTTATAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (25 bp):
CATGAGCTTCATGATATATGGCTCG
Found at i:315249 original size:11 final size:12
Alignment explanation
Indices: 315226--315259 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
315216 GAAATCTAGG
315226 TGGATTCTTTCC
1 TGGATTCTTTCC
315238 TGGATT-TTTCC
1 TGGATTCTTTCC
315249 TGGATTCTTTC
1 TGGATTCTTTC
315260 TTGGGTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.09, C:0.21, G:0.18, T:0.53
Consensus pattern (12 bp):
TGGATTCTTTCC
Found at i:321919 original size:19 final size:19
Alignment explanation
Indices: 321895--321934 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
321885 AATTTCGTGG
321895 ACATCACATAGTACCTCAC
1 ACATCACATAGTACCTCAC
321914 ACATCACATAGTACCTCAC
1 ACATCACATAGTACCTCAC
321933 AC
1 AC
321935 CCATTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.38, G:0.05, T:0.20
Consensus pattern (19 bp):
ACATCACATAGTACCTCAC
Found at i:329532 original size:22 final size:22
Alignment explanation
Indices: 329498--329575 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
329488 TTTCACTTTT
329498 TCAATTCACTCTCAACT-CTCTC
1 TCAATTCACTCTCAA-TGCTCTC
* *
329520 TCAATTTATTCTCAATGCTCTC
1 TCAATTCACTCTCAATGCTCTC
* * *
329542 TTAATTCTCACTCAAT--TCTC
1 TCAATTCACTCTCAATGCTCTC
* *
329562 TTAGTTCACTCTCA
1 TCAATTCACTCTCA
329576 TGTTTTGTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.33
21 1 0.02
22 29 0.64
ACGTcount: A:0.23, C:0.32, G:0.03, T:0.42
Consensus pattern (22 bp):
TCAATTCACTCTCAATGCTCTC
Found at i:329771 original size:18 final size:20
Alignment explanation
Indices: 329750--329788 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
329740 AATAATGTTA
329750 TTTATAA-AACTC-AAAATT
1 TTTATAACAACTCTAAAATT
329768 TTTATAACAACTCTAAAATT
1 TTTATAACAACTCTAAAATT
329788 T
1 T
329789 ATACTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTATAACAACTCTAAAATT
Found at i:329836 original size:20 final size:19
Alignment explanation
Indices: 329813--329859 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
329803 CTATAAATAT
329813 TATAAAAAAATCTTAAAGAA
1 TATAAAAAAATCTTAAA-AA
* *
329833 TATATAAAAATGTTAAAAA
1 TATAAAAAAATCTTAAAAA
329852 -ATAAAAAA
1 TATAAAAAA
329860 TTCCCTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.29
19 2 0.08
20 15 0.62
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
TATAAAAAAATCTTAAAAA
Found at i:337571 original size:31 final size:31
Alignment explanation
Indices: 337530--337604 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
337520 TTTAAAGGTA
* * *
337530 AAGTAACTAAAATTTACAACTTATTTAA-TAG
1 AAGTGACTAAAATTGACAACTTATCTAACT-G
*
337561 AAGTGACTAAAATTGACAATTTATCTAACTG
1 AAGTGACTAAAATTGACAACTTATCTAACTG
*
337592 GAGTGACTAAAAT
1 AAGTGACTAAAAT
337605 AATCAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (31 bp):
AAGTGACTAAAATTGACAACTTATCTAACTG
Found at i:341094 original size:72 final size:72
Alignment explanation
Indices: 340977--341118 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 72
340967 CTCGGATCTA
* * ***
340977 AAAAAGGGATCATGCCGAGTAAGTTAGGACACAATCTTTTCTTAATTCTTGAGATCGTTTAAAAC
1 AAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCAAGATCGTTTAAAAC
341042 TTGAGAG
66 TTGAGAG
* *
341049 AAAAAGGGATCATGCCCAGTAAGTTATGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAAC
1 AAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCAAGATCGTTTAAAAC
341114 TTGAG
66 TTGAG
341119 TTTGAAAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (72 bp):
AAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCAAGATCGTTTAAAAC
TTGAGAG
Found at i:341483 original size:38 final size:35
Alignment explanation
Indices: 341432--341517 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 35
341422 GGTATATGCG
* *
341432 TATATATATATAAAGTATAAATAATATATAGGTATGTA
1 TATATATATATAAA-T-TAAAAAAAAT-TAGGTATGTA
*
341470 TATATATATATAAATTAAAAAAAATTATGTATGTA
1 TATATATATATAAATTAAAAAAAATTAGGTATGTA
341505 TATATAT-TATAAA
1 TATATATATATAAA
341518 AAATGTATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 6 0.13
35 16 0.36
36 8 0.18
37 1 0.02
38 14 0.31
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (35 bp):
TATATATATATAAATTAAAAAAAATTAGGTATGTA
Found at i:341531 original size:28 final size:27
Alignment explanation
Indices: 341476--341539 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
341466 TGTATATATA
* *
341476 TATATAAATTAAAAAAAATTATGTATG
1 TATATATATTAAAAAAAATTATGCATG
*
341503 TATATATATTATAAAAAATGTATGCATG
1 TATATATATTAAAAAAAAT-TATGCATG
*
341531 TATGTATAT
1 TATATATAT
341540 ATACATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (27 bp):
TATATATATTAAAAAAAATTATGCATG
Found at i:341617 original size:31 final size:29
Alignment explanation
Indices: 341578--341638 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 29
341568 ACATAAATGA
341578 GTAAATAAT-GATAATAATAATATTAACAAT
1 GTAAATAATAG-TAATAATAATATTAA-AAT
*
341608 GTAATATAATAGTAATAATGATATTAAAAT
1 GTAA-ATAATAGTAATAATAATATTAAAAT
341638 G
1 G
341639 ATCAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.29
31 19 0.68
32 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (29 bp):
GTAAATAATAGTAATAATAATATTAAAAT
Found at i:343305 original size:138 final size:135
Alignment explanation
Indices: 343105--343406 Score: 408
Period size: 138 Copynumber: 2.2 Consensus size: 135
343095 GGTTTTAGTT
* * * * *
343105 TGCTCCACTACAACGTCAGGGAGATAAGACTTGTCATGGTAGATTTAACCTGACCTACTGCAACT
1 TGCTCTACTGCAACTTCAGGGAGATAAGACTTATCATGGTAGATTTAACCTGACCTACTGCAAAT
*
343170 TCAGAAGTATAGGATTCATCATTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGA-TTAGTA
66 TCAGAAGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTTA-T-
*
343234 GCTTCAGTC
129 -CGTCA-TC
* *
343243 TGCTCTACTGCAACTTCAGGGAGATAAGACTTATTATGGTAGATTTAATCTGACCTACTGCAAAT
1 TGCTCTACTGCAACTTCAGGGAGATAAGACTTATCATGGTAGATTTAACCTGACCTACTGCAAAT
* * * * * *
343308 TTAGATGTATAGGATTTATCATTTTAATCCGGTCCACTGTAACTTGAGGGAGATAGGACTTATCG
66 TCAGAAGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTTATCG
*
343373 TGATC
131 TCATC
*
343378 TGCTCTACTGCAACTTCAGAGAGATAAGA
1 TGCTCTACTGCAACTTCAGGGAGATAAGA
343407 TATGCTATCT
Statistics
Matches: 146, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
135 30 0.21
136 3 0.02
138 110 0.75
139 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (135 bp):
TGCTCTACTGCAACTTCAGGGAGATAAGACTTATCATGGTAGATTTAACCTGACCTACTGCAAAT
TCAGAAGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGACTTATCG
TCATC
Found at i:343706 original size:45 final size:44
Alignment explanation
Indices: 343522--344139 Score: 198
Period size: 44 Copynumber: 13.8 Consensus size: 44
343512 TCATCATTTT
* * * *
343522 AATCCGCTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTC
* * * * * *
343566 AATTTGTTCCACTACAACTTTAGGGAAATAAGA-TTGGAT-TAGTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCT--TC
* * * * *
343610 AGTCTGCTTCACTGCGACTTCAGAGAGATAAGACTTGT-TGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAT--CTTC
*
343655 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TATCTTC
* * * * * * *
343700 AGTCTGCCCCATTGCAACTTTAGGGGGATAAGACTTACTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTC
* * * *
343745 AAT-T--T-TAATG---C--CAGGGAGATAAGATTCGTTGCCTTCAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA--C-TTG---T-ATCTTC
* * * * *
343787 AATTTGCTCCACTGCAA-TGCCAGGGAAACAAGA-TTCGCTACCTTTAGCTTT
1 AATCTGCTCCACTGCAACT-TCAGGGAGATAAGACTT-G-TA----T--CTTC
* ** ** ** * * *
343838 AATCTGTTCCACTATAACGCCAATGAGATAAGTCTGGTGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTC
** * * * * ** *
343882 AATCCACTCCATTACAATTTCAGAGAGATAAGA--TCCATCATTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATC--TTC
* * * *
343926 AATCTGCTCCACTGCAACTTCAGGGAGGTAGGA-TTAGTAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTC
* **
343970 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTAGTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTC
* ** *
344014 AGTCTGCTCCACTATAACTTTAGGGAGATAAGACTTGT-TGGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAT--CTTC
* * ** *
344059 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTCCCATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTC
*
344104 AGTCTG-TCCCACTGCAACTTCAGAGG-GATAAGACTT
1 AATCTGCT-CCACTGCAACTTCAG-GGAGATAAGACTT
344140 ACTTTCTTCA
Statistics
Matches: 413, Mismatches: 115, Indels: 91
0.67 0.19 0.15
Matches are distributed among these distances:
36 11 0.03
38 2 0.00
39 2 0.00
41 4 0.01
42 9 0.02
43 5 0.01
44 177 0.43
45 147 0.36
46 10 0.02
47 5 0.01
48 1 0.00
50 1 0.00
51 38 0.09
52 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTC
Found at i:343836 original size:51 final size:51
Alignment explanation
Indices: 343751--343850 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
343741 CTTCAATTTT
* * * * *
343751 AATGCCAGGGAGATAAGATTCGTTGCCTTCAGCTTTAATTTGCTCCACTGC
1 AATGCCAGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACTGC
* *
343802 AATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACT
1 AATGCCAGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACT
343851 ATAACGCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (51 bp):
AATGCCAGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACTGC
Found at i:344316 original size:404 final size:404
Alignment explanation
Indices: 343490--344409 Score: 1242
Period size: 404 Copynumber: 2.3 Consensus size: 404
343480 TCTGCTCTAT
* * *
343490 TGCAACTTTAGATAGATAAGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
1 TGCAACTTTAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGGTAGGA
* * * * * * *
343555 CTAGTAACTTCAATTTGTTCCACTACAACTTTAGGGAAATAAGATTGGATTAGTCAGTCTGCTTC
66 TTAGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATTAGTCAGTCTGCTCC
* * *
343620 ACTGCGACTTCAGAGAGATAAGACTTGTTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
131 ACTACAACTTCAGAGAGATAAGACTTGTTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* * * * *
343685 AGATTTGCTATCTTCAGTCTGCCCCATTGCAACTTTAGGGGGATAAGACTTACTTTCTTCAATTT
196 AGATTTCCCATCTTCAGTCTGCCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCTTCAATTT
* * *
343750 TAATGCCAGGGAGATAAGATTCGTTGCCTTCAGCTTTAATTTGCTCCACTGCAATGCCAGGGAAA
261 TAATGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAATGCCAGGGAAA
** *
343815 CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAACGCCAATGAGATAAGTCTGGTGTCT
326 CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAACGCCAATGAGATAAGTCTACTATCT
*
343880 TCAATCCACTCCAT
391 TCAATCCACTCCAC
* *
343894 TACAA-TTTCAGAGAGATAAGATCCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGGTAGG
1 TGCAACTTT-AGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGGTAGG
* *
343958 ATTAGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTAGTCAGTCTGCTC
65 ATTAGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATTAGTCAGTCTGCTC
* * * *
344023 CACTATAACTTTAGGGAGATAAGACTTGTTGGCTTCAATCTGCTCCACTGCAACTTTAGGGAGAT
130 CACTACAACTTCAGAGAGATAAGACTTGTTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
* *
344088 AAGATTTCCCATCTTTAGTCTGTCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCTTCAATT
195 AAGATTTCCCATCTTCAGTCTGCCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCTTCAATT
* *
344153 TTAATGCCAGAGAGATAAGATTTGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAATG-CAGGGAA
260 TTAATGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAATGCCAGGGAA
* * * *
344217 ACAAGATTCGCTACCTTTAGTTTTAATCTGTTCCACTGTAACGCCAATGGGATAGGAT-TCACTA
325 ACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAACGCCAATGAGATAAG-TCT-ACTA
* **
344281 TCTTCAGTCTTCTCCAC
388 TCTTCAATCCACTCCAC
* ** * *
344298 TGCAACTTTAGGGAGATAAGACTTTGTACGA--TCAATCTGCCCCACTGCAACTTCAGGG-GGAT
1 TGCAACTTTAGAGAGATAAGA-TTCAT-C-ATTTTAATCTGCTCCACTGCAACTTCAGGGAGG-T
* * * *
344360 AAGATTAGTGA-TTTCAATCTACTCCACTGCAACTTTAGGAAGATAAGATT
62 AGGATTAGTAACTTT-AATCTGCTCCACTGCAACTTTAGGGAGATAAGATT
344410 CGCCATGACG
Statistics
Matches: 451, Mismatches: 56, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
403 63 0.14
404 314 0.70
405 72 0.16
406 1 0.00
407 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (404 bp):
TGCAACTTTAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGGTAGGA
TTAGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGATTAGTCAGTCTGCTCC
ACTACAACTTCAGAGAGATAAGACTTGTTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
AGATTTCCCATCTTCAGTCTGCCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCTTCAATTT
TAATGCCAGAGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCACTGCAATGCCAGGGAAA
CAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAACGCCAATGAGATAAGTCTACTATCT
TCAATCCACTCCAC
Found at i:344392 original size:44 final size:44
Alignment explanation
Indices: 344283--344409 Score: 141
Period size: 44 Copynumber: 2.9 Consensus size: 44
344273 ATTCACTATC
* * *
344283 TTCAGTCTTCTCCACTGCAACTTTAGGGAGATAAGACTTTGTACGA
1 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGA-TTAGTA-GA
* * * *
344329 -TCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGT-GA
1 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTAGTAGA
*
344371 TTTCAATCTACTCCACTGCAACTTTAGGAAGATAAGATT
1 -TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATT
344410 CGCCATGACG
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.03
44 36 0.53
45 30 0.44
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTAGTAGA
Found at i:344516 original size:51 final size:51
Alignment explanation
Indices: 344435--344581 Score: 177
Period size: 51 Copynumber: 2.9 Consensus size: 51
344425 AACTTTAACG
* ** *
344435 CCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTGCTGCAATA
1 CCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACTGCAACA
* * * * *
344486 CCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGTAACA
1 CCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACTGCAACA
* * * *
344537 CCAAGGAGATAGGATTCACTACCTTCAGCTTTAATCCGCTCCACT
1 CCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACT
344582 TCAGCTTTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 79 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (51 bp):
CCAGGGAGATAAGATTCGCTACCTTCAGCTTTAATCTGCTCCACTGCAACA
Found at i:344883 original size:132 final size:132
Alignment explanation
Indices: 344663--345295 Score: 845
Period size: 132 Copynumber: 4.8 Consensus size: 132
344653 TGCAAAGCCA
* * ** *
344663 GGAAAATAAGAGTCGCTTTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
* * * * *
344728 TCAACATACTCCACAGCTACTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCTCTACTACCT
66 TCAACCTACTCTACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
344793 TG
131 TG
* * * * * * *
344795 GGAAGATAAGATTCACCGTCTTCGATCTACTCCTCTACTTCTTAGGTAGACAAGATCTACAATCC
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
* * * *
344860 TCAACCTACTCTACTGCTGCTCAGGGAGATAGAATTGGTGGCCTAAATTTGCTTCCCTACTACCT
66 TCAACCTACTCTACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
344925 TG
131 TG
* * * * *
344927 GGAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGATACATGATCTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
* * *
344992 TCAACCTACTCTACTGCTGCTCAGGGAGATAGAACCGGTGGCTTAAATCTGCTTTCCTACTACCT
66 TCAACCTACTCTACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
345057 TG
131 TG
* * * * *
345059 GGAAGATAAGATTTGTCGTATTCAACCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
* *
345124 TCAACCTACTGTACTGCTGCTCAGGGAGATAAGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
66 TCAACCTACTCTACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
345189 TG
131 TG
* * * * * * *
345191 GGAAGATAAGATTCGTCGGCTTCGATCTTCTCTACTACTGCTTAGGGAGATATGATTTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
* *
345256 TCAACCTACTCCACTACTGCTCAGGGAGATAAGG-CTGGTG
66 TCAACCTACTCTACTGCTGCTCAGGGAGAT-AGGACTGGTG
345296 CTTTTGATCT
Statistics
Matches: 436, Mismatches: 64, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
132 434 1.00
133 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCT
TCAACCTACTCTACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
TG
Found at i:346702 original size:13 final size:12
Alignment explanation
Indices: 346677--346710 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
346667 GTGACCTCTC
*
346677 CTTTTTCTTTTT
1 CTTTTTTTTTTT
346689 CTTTTCTTTTTTT
1 CTTTT-TTTTTTT
346702 CTTTTTTTT
1 CTTTTTTTT
346711 GAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:349740 original size:73 final size:74
Alignment explanation
Indices: 349621--349763 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 74
349611 TCTCGGATTT
* *
349621 AAAAAAGGATCATGCCGAGTAAGTTAGGACACGATCTTTTCTTAATT-CCAAGTTCGTTTAAAAC
1 AAAAAAGGATCATGCCGAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAAC
349685 TTGAGAGAA
66 TTGAGAGAA
349694 AAAAAAGGGATCATGCC-AGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
1 AAAAAA-GGATCATGCCGAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
349758 CTTGAG
65 CTTGAG
349764 TTTGAAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 35 0.53
74 31 0.47
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (74 bp):
AAAAAAGGATCATGCCGAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAAC
TTGAGAGAA
Found at i:350093 original size:22 final size:22
Alignment explanation
Indices: 350068--350112 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
350058 ATTAAAACGT
350068 TCTTTCAAAATAATAATGAACA
1 TCTTTCAAAATAATAATGAACA
350090 TCTTTCAAAATAATAATGAACA
1 TCTTTCAAAATAATAATGAACA
350112 T
1 T
350113 GTAAATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (22 bp):
TCTTTCAAAATAATAATGAACA
Found at i:350226 original size:14 final size:12
Alignment explanation
Indices: 350199--350242 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
350189 AATTAAAAAG
*
350199 TATGTATGTATA
1 TATGTATATATA
**
350211 TGCGTATATATA
1 TATGTATATATA
350223 TATGTATATATA
1 TATGTATATATA
*
350235 TAAGTATA
1 TATGTATA
350243 AAGTGGTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (12 bp):
TATGTATATATA
Found at i:350321 original size:4 final size:4
Alignment explanation
Indices: 350314--350413 Score: 191
Period size: 4 Copynumber: 25.0 Consensus size: 4
350304 ATATTATAAA
350314 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
350362 GTAT GTAT GTAT GTAT GAAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
350410 GTAT
1 GTAT
350414 AACAAAATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:354127 original size:17 final size:16
Alignment explanation
Indices: 354105--354148 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
354095 AATTAATTTA
*
354105 ACATATTTAGATTATTC
1 ACATATTTAGATT-TGC
354122 ACATATTTAG-TTTGC
1 ACATATTTAGATTTGC
*
354137 ATATATTTAGAT
1 ACATATTTAGAT
354149 CACATCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 10 0.42
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (16 bp):
ACATATTTAGATTTGC
Found at i:358120 original size:18 final size:18
Alignment explanation
Indices: 358047--358122 Score: 84
Period size: 18 Copynumber: 4.1 Consensus size: 18
358037 TGAATTTATT
358047 AAAATTAAAAAAT-TAAA
1 AAAATTAAAAAATATAAA
* *
358064 TATAAATTCAAAAATAAGAAA
1 -A-AAATTAAAAAAT-ATAAA
358085 AAAATTAAAAAA-ATTAAA
1 AAAATTAAAAAATA-TAAA
358103 AAAATTAAAAAATATAAA
1 AAAATTAAAAAATATAAA
358121 AA
1 AA
358123 TGTTATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.02
18 22 0.45
19 22 0.45
20 1 0.02
21 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (18 bp):
AAAATTAAAAAATATAAA
Found at i:358122 original size:9 final size:9
Alignment explanation
Indices: 358047--358114 Score: 77
Period size: 9 Copynumber: 7.3 Consensus size: 9
358037 TGAATTTATT
358047 AAAATT-AA
1 AAAATTAAA
358055 AAAATTAAA
1 AAAATTAAA
358064 TATAAATTCAAA
1 -A-AAATT-AAA
*
358076 AATAA-GAAA
1 AA-AATTAAA
358085 AAAATTAAA
1 AAAATTAAA
358094 AAAATTAAA
1 AAAATTAAA
358103 AAAATTAAA
1 AAAATTAAA
358112 AAA
1 AAA
358115 TATAAAAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.15
9 31 0.60
10 2 0.04
11 8 0.15
12 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (9 bp):
AAAATTAAA
Found at i:358263 original size:26 final size:26
Alignment explanation
Indices: 358234--358283 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
358224 CTCTATTTAT
358234 AGACATAAGAAGTATAAATAAAGTAG
1 AGACATAAGAAGTATAAATAAAGTAG
*
358260 AGACATAAGAAGTATAAATGAAGT
1 AGACATAAGAAGTATAAATAAAGT
358284 CTACTTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (26 bp):
AGACATAAGAAGTATAAATAAAGTAG
Found at i:358456 original size:18 final size:18
Alignment explanation
Indices: 358426--358467 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
358416 TTACTAAGAT
*
358426 AAAAACCTTGTG-AGAAA
1 AAAAATCTTGTGAAGAAA
358443 AAAAATCTTAGTGAAGAAA
1 AAAAATCTT-GTGAAGAAA
358462 AAAAAT
1 AAAAAT
358468 ACACATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 3 0.14
19 11 0.50
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (18 bp):
AAAAATCTTGTGAAGAAA
Found at i:360476 original size:16 final size:16
Alignment explanation
Indices: 360422--360479 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
360412 ACGATTTTTT
* *
360422 TAAAATAAATAATATG
1 TAAAATAAATTATATA
* *
360438 TACAAA-AATTTACATA
1 TA-AAATAAATTATATA
*
360454 TAGAATAAATTATATA
1 TAAAATAAATTATATA
360470 TAAAATAAAT
1 TAAAATAAAT
360480 AAATTGTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 2 0.06
16 27 0.84
17 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAAATAAATTATATA
Found at i:364295 original size:26 final size:26
Alignment explanation
Indices: 364257--364318 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
364247 CCTACAGTAA
* *
364257 TTTCAGAATATCATAACATTTATCAG
1 TTTCAGAACATCATAACATGTATCAG
* *
364283 TTTCATAACATCATAGCATGTATCAG
1 TTTCAGAACATCATAACATGTATCAG
364309 TTTCAGAACA
1 TTTCAGAACA
364319 CTTACAGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (26 bp):
TTTCAGAACATCATAACATGTATCAG
Found at i:368988 original size:25 final size:25
Alignment explanation
Indices: 368960--369033 Score: 130
Period size: 25 Copynumber: 3.0 Consensus size: 25
368950 TATGCTCTCT
*
368960 CGAGCTGTGAATCGGTAAGCTCATA
1 CGAGCTGAGAATCGGTAAGCTCATA
368985 CGAGCTGAGAATCGGTAAGCTCATA
1 CGAGCTGAGAATCGGTAAGCTCATA
*
369010 CGAGCTGAAAATCGGTAAGCTCAT
1 CGAGCTGAGAATCGGTAAGCTCAT
369034 GAGAGATGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (25 bp):
CGAGCTGAGAATCGGTAAGCTCATA
Found at i:370566 original size:2 final size:2
Alignment explanation
Indices: 370559--370608 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
370549 ATAAAGCATA
370559 AT AT AT AT -T ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
370600 AT AT A- AT AT
1 AT AT AT AT AT
370609 TNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 40 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371785 original size:40 final size:40
Alignment explanation
Indices: 371730--371810 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
371720 ATAATATAAG
371730 TGACATTGATACATGCCTTGAAACCTTCGTTAATTTCTTA
1 TGACATTGATACATGCCTTGAAACCTTCGTTAATTTCTTA
371770 TGACATTGATACATGCCTTGAAACCTTCGTTAATTTCTTA
1 TGACATTGATACATGCCTTGAAACCTTCGTTAATTTCTTA
371810 T
1 T
371811 AAATTTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (40 bp):
TGACATTGATACATGCCTTGAAACCTTCGTTAATTTCTTA
Found at i:398659 original size:17 final size:18
Alignment explanation
Indices: 398637--398671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
398627 ATATGGGTCA
*
398637 TGTGGG-CCACACGGGCG
1 TGTGGGCCCACACAGGCG
398654 TGTGGGCCCACACAGGCG
1 TGTGGGCCCACACAGGCG
398672 AACATCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.31, G:0.43, T:0.11
Consensus pattern (18 bp):
TGTGGGCCCACACAGGCG
Found at i:399664 original size:18 final size:18
Alignment explanation
Indices: 399611--399664 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
399601 GTAATAAGAA
399611 AATGTTTT-GAAATTGAAT
1 AATGTTTTGGAAA-TGAAT
* * *
399629 AACGATTTGTAAATGAAT
1 AATGTTTTGGAAATGAAT
*
399647 AATGTTTTGGAAACGAAT
1 AATGTTTTGGAAATGAAT
399665 GACATGATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 25 0.89
19 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.37
Consensus pattern (18 bp):
AATGTTTTGGAAATGAAT
Found at i:401341 original size:17 final size:17
Alignment explanation
Indices: 401302--401338 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
401292 AATATCTAGA
401302 TAAATATTAAATTAAAT
1 TAAATATTAAATTAAAT
*
401319 TTAATATTAAATT-AAT
1 TAAATATTAAATTAAAT
401335 TAAA
1 TAAA
401339 ATAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:401453 original size:72 final size:72
Alignment explanation
Indices: 401370--401505 Score: 272
Period size: 72 Copynumber: 1.9 Consensus size: 72
401360 TTAATTTGAA
401370 ATCAAGCTACCTGTTAGAGTCCCACTAATATTCTAATTTTTTTCACTACTTTACCATTGAAGAAA
1 ATCAAGCTACCTGTTAGAGTCCCACTAATATTCTAATTTTTTTCACTACTTTACCATTGAAGAAA
401435 TTAATTT
66 TTAATTT
401442 ATCAAGCTACCTGTTAGAGTCCCACTAATATTCTAATTTTTTTCACTACTTTACCATTGAAGAA
1 ATCAAGCTACCTGTTAGAGTCCCACTAATATTCTAATTTTTTTCACTACTTTACCATTGAAGAA
401506 CCACTACTGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (72 bp):
ATCAAGCTACCTGTTAGAGTCCCACTAATATTCTAATTTTTTTCACTACTTTACCATTGAAGAAA
TTAATTT
Found at i:414038 original size:18 final size:18
Alignment explanation
Indices: 414015--414067 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
414005 GTGTTGCCCC
414015 ACGTTTGTCTGCGATCAT
1 ACGTTTGTCTGCGATCAT
* *
414033 ACGTTTGTCTACGATCGT
1 ACGTTTGTCTGCGATCAT
414051 ACGTTTGTCTGCGATCA
1 ACGTTTGTCTGCGATCA
414068 CTCGGTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (18 bp):
ACGTTTGTCTGCGATCAT
Found at i:418107 original size:19 final size:19
Alignment explanation
Indices: 418083--418123 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
418073 CTTCTTGCTT
418083 GGACGAATACACCATTGAA
1 GGACGAATACACCATTGAA
418102 GGACGAATACACCATTGAA
1 GGACGAATACACCATTGAA
418121 GGA
1 GGA
418124 GGGAGCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (19 bp):
GGACGAATACACCATTGAA
Found at i:418727 original size:16 final size:16
Alignment explanation
Indices: 418703--418763 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
418693 TAGTGTTATT
418703 CAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCTAG
*
418719 CAGGTTTTGTGCCTAG
1 CAGGCTTTGTGCCTAG
*
418735 CAGGCTTTGTGCTTAG
1 CAGGCTTTGTGCCTAG
418751 CAGGCTTTGTGCC
1 CAGGCTTTGTGCC
418764 GGTGTTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.11, C:0.23, G:0.31, T:0.34
Consensus pattern (16 bp):
CAGGCTTTGTGCCTAG
Found at i:418790 original size:38 final size:38
Alignment explanation
Indices: 418738--418838 Score: 141
Period size: 38 Copynumber: 2.7 Consensus size: 38
418728 TGCCTAGCAG
* *
418738 GCTTTGTGCTTAGCAGGCTTTGTGCCGGTGTTATTCAA
1 GCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATCCAA
*
418776 GCTTTGCT-CCTAGCAGGCTTTGTGCCGGTGTTATCCAG
1 GCTTTG-TGCCTAGCAGGCTTTGTGCCGGTGTTATCCAA
* *
418814 GCTTTGTGCCTAGCAAGCTTAGTGC
1 GCTTTGTGCCTAGCAGGCTTTGTGC
418839 AGTGTATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.02
38 54 0.96
39 1 0.02
ACGTcount: A:0.13, C:0.23, G:0.29, T:0.36
Consensus pattern (38 bp):
GCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATCCAA
Found at i:419754 original size:50 final size:51
Alignment explanation
Indices: 419695--419790 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 51
419685 TTTATAAAGT
* * *
419695 CATGTATTATAAAACTCTCATGTTAGTT-AAGATTGCATCATAAATTATGA
1 CATGCATTATAAAACCCTCATGATAGTTAAAGATTGCATCATAAATTATGA
** * *
419745 CATGCATTATGTAACCCTCATGATAGTTAAAGTTTGCATCTTAAAT
1 CATGCATTATAAAACCCTCATGATAGTTAAAGATTGCATCATAAAT
419791 GAAGTCACGC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 23 0.61
51 15 0.39
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (51 bp):
CATGCATTATAAAACCCTCATGATAGTTAAAGATTGCATCATAAATTATGA
Found at i:427756 original size:22 final size:22
Alignment explanation
Indices: 427728--427802 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
427718 TTGTGCCTAG
* * *
427728 CAGGCTTCGTGCTGGTGTTAAT
1 CAGGCTTTGTGCCGGTGTTATT
427750 CAGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCCGGTGTTATT
*
427772 CTA-GCTTTGTGCCGATGTTATT
1 C-AGGCTTTGTGCCGGTGTTATT
427794 CAGGCTTTG
1 CAGGCTTTG
427803 CTCCTAGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.02
22 45 0.96
23 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (22 bp):
CAGGCTTTGTGCCGGTGTTATT
Found at i:427762 original size:38 final size:38
Alignment explanation
Indices: 427708--427868 Score: 148
Period size: 38 Copynumber: 4.1 Consensus size: 38
427698 ATTATATTGC
* *
427708 TATTCAGGCTTTGTGCCTAGCAGGCTTCGTGCTGGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGT
* * *
427746 TAATCAGGCTTTGTGCCGGTGTTATTCTA-GCTTTGTGCCGATGT
1 TATTCAGGCTTTGTGCC-----TA-GC-AGGCTTTGTGCCGGTGT
* *
427790 TATTCAGGCTTTGCT-CCTAGCAGGCTTTGTACCAGTGT
1 TATTCAGGCTTTG-TGCCTAGCAGGCTTTGTGCCGGTGT
* *
427828 TATTCAGGCTTTGTGCCTAGCAAGCTTAGTGCCGGT-T
1 TATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGT
427865 TATT
1 TATT
427869 AAAAGTTAAC
Statistics
Matches: 99, Mismatches: 14, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
37 7 0.07
38 59 0.60
39 2 0.02
43 2 0.02
44 27 0.27
45 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (38 bp):
TATTCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGT
Found at i:434263 original size:2 final size:2
Alignment explanation
Indices: 434256--434289 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
434246 TTAAGATTTA
434256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434290 GCTTTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435280 original size:14 final size:14
Alignment explanation
Indices: 435258--435300 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
435248 TACAAACTTA
435258 TTAAGTAAATTATT
1 TTAAGTAAATTATT
*
435272 TTAACTAAA-TATT
1 TTAAGTAAATTATT
435285 TT-AGTAAAATTATT
1 TTAAGT-AAATTATT
435299 TT
1 TT
435301 TTTTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 2 0.08
13 9 0.36
14 14 0.56
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (14 bp):
TTAAGTAAATTATT
Found at i:435338 original size:19 final size:18
Alignment explanation
Indices: 435301--435348 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
435291 AAATTATTTT
* *
435301 TTTTATAAATGTGATAAA
1 TTTTATAAATGTAAAAAA
435319 TTTTATAAATAGTAAAAAA
1 TTTTATAAAT-GTAAAAAA
435338 TATTTA-AAATG
1 T-TTTATAAATG
435349 GAAATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 11 0.42
19 11 0.42
20 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTTATAAATGTAAAAAA
Found at i:437985 original size:21 final size:21
Alignment explanation
Indices: 437941--437986 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
437931 AATATTAAAT
*
437941 TTAATCTAATATTTATCTTGA
1 TTAATCTAATATTAATCTTGA
*
437962 TTAATTTAATATTAAATCTT-A
1 TTAATCTAATATT-AATCTTGA
437983 TTAA
1 TTAA
437987 AATAGTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATCTAATATTAATCTTGA
Found at i:439720 original size:20 final size:20
Alignment explanation
Indices: 439695--439732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
439685 TAATATTTGT
*
439695 TTGTCACAATTTTGCTATAC
1 TTGTCACAATTTTACTATAC
439715 TTGTCACAATTTTACTAT
1 TTGTCACAATTTTACTAT
439733 GCATGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.47
Consensus pattern (20 bp):
TTGTCACAATTTTACTATAC
Found at i:458156 original size:16 final size:16
Alignment explanation
Indices: 458135--458173 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
458125 TTGATTTGCT
*
458135 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
458151 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
458167 ATTACAC
1 ATTACAC
458174 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:458174 original size:16 final size:16
Alignment explanation
Indices: 458148--458204 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
458138 ACACAGCTTT
* *
458148 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
458164 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
458180 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
458196 TCCAATACA
1 TCCAATACA
458205 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:459400 original size:20 final size:20
Alignment explanation
Indices: 459375--459412 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
459365 TATATATATG
459375 TATATAGAAAT-TATGAAATA
1 TATATA-AAATATATGAAATA
459395 TATATAAAATATATGAAA
1 TATATAAAATATATGAAA
459413 GTGTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
TATATAAAATATATGAAATA
Found at i:460068 original size:73 final size:72
Alignment explanation
Indices: 459957--460456 Score: 547
Period size: 72 Copynumber: 6.9 Consensus size: 72
459947 CGTTTTCGAT
* * * *
459957 AAAGCGCCGCAAAAAAT--CCCAAACGCGTCGTTTTGATTTGAGATGTAGTGGCATTAGTGGCGA
1 AAAGCGCCGCAAAAAATAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGC
460020 TTCCGTA
66 TTCCGTA
* * * * *
460027 AAAACGCCGCAAAAAAATAACCCAAACGCTTCGTTTTGATTTGAGATGTTGTGGCGTTAGCGGCG
1 AAAGCGCCGC-AAAAAATAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCG
* **
460092 ATTCCACA
65 CTTCCGTA
*** * * * *
460100 AAAGCATAGCAAAAAATAATCAAAACACATCGTTTTGATTTGGGATGTAGTTGCATTAGCGGCGC
1 AAAGCGCCGCAAAAAATAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGC
*
460165 TTCCATA
66 TTCCGTA
* ** * * * *
460172 AAAGCGCAGCAAGGAATAACCAAAACACATCTTTTTGATTTCAGATGTAATGGCATTAGCGGCGC
1 AAAGCGCCGCAAAAAATAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGC
*
460237 TTCTGTA
66 TTCCGTA
* * * * *
460244 TAAGCGCCACAAAAAACAAACCAAAACGCATCGTTTTGATATGAGATGTAGTGGCATCAGCGGCG
1 AAAGCGCCGCAAAAAA-TAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCG
*
460309 CTTCTGTA
65 CTTCCGTA
* * *
460317 AAAGCGCCACCAAAAAA-AACCCAAAACGCATCGTTTTGGTTTCAGATGTAGTGGCATTAGCGGC
1 AAAGCGCC-GCAAAAAATAA-CCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGC
*
460381 GCTTCTGTA
64 GCTTCCGTA
* * * * * *
460390 AAACCGCCACAAAAAATAATCAAAACGCATCGTTTTGATTTGAGATGCAGTGGTATTAGTGGCGC
1 AAAGCGCCGCAAAAAATAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGC
460455 TT
66 TT
460457 TTCTTGAAAA
Statistics
Matches: 364, Mismatches: 59, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
70 9 0.02
71 7 0.02
72 174 0.48
73 167 0.46
74 7 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (72 bp):
AAAGCGCCGCAAAAAATAACCAAAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGC
TTCCGTA
Found at i:460158 original size:145 final size:142
Alignment explanation
Indices: 459977--460456 Score: 548
Period size: 145 Copynumber: 3.3 Consensus size: 142
459967 AAAAAATCCC
* * * *
459977 AAACGCGTCGTTTTGATTTGAGATGTAGTGGCATTAGTGGCGATTCCGTAAAAACGCCGCAAAAA
1 AAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGCTTCCGTAAAAGCGCCGC-AAAA
* * * * * *** *
460042 AATAACCCAAACGCTTCGTTTTGATTTGAGATGTTGTGGCGTTAGCGGCGATTCCACAAAAGCAT
65 AATAACCCAAACGCATCGTTTTGATTTCAGATGTAGTGGCATTAGCGGCGCTTCTGTAAAAGC-C
460107 AGCAAAAAATAATCA
129 A-CAAAAAATAATCA
* * * * * **
460122 AAACACATCGTTTTGATTTGGGATGTAGTTGCATTAGCGGCGCTTCCATAAAAGCGCAGCAAGGA
1 AAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGCTTCCGTAAAAGCGCCGCAAAAA
* * * * *
460187 ATAACCAAAACACATCTTTTTGATTTCAGATGTAATGGCATTAGCGGCGCTTCTGTATAAGCGCC
66 ATAACCCAAACGCATCGTTTTGATTTCAGATGTAGTGGCATTAGCGGCGCTTCTGTA-AA-AGCC
* *
460252 ACAAAAAACAAACCA
129 ACAAAAAA-TAATCA
* * * *
460267 AAACGCATCGTTTTGATATGAGATGTAGTGGCATCAGCGGCGCTTCTGTAAAAGCGCCACCAAAA
1 AAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGCTTCCGTAAAAGCGCC-GCAAAA
*
460332 AA-AACCCAAAACGCATCGTTTTGGTTTCAGATGTAGTGGCATTAGCGGCGCTTCTGTAAAACCG
65 AATAACCC-AAACGCATCGTTTTGATTTCAGATGTAGTGGCATTAGCGGCGCTTCTGTAAAA--G
460396 CCACAAAAAATAATCA
127 CCACAAAAAATAATCA
* * *
460412 AAACGCATCGTTTTGATTTGAGATGCAGTGGTATTAGTGGCGCTT
1 AAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGCTT
460457 TTCTTGAAAA
Statistics
Matches: 277, Mismatches: 51, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
144 55 0.20
145 158 0.57
146 64 0.23
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (142 bp):
AAACGCATCGTTTTGATTTGAGATGTAGTGGCATTAGCGGCGCTTCCGTAAAAGCGCCGCAAAAA
ATAACCCAAACGCATCGTTTTGATTTCAGATGTAGTGGCATTAGCGGCGCTTCTGTAAAAGCCAC
AAAAAATAATCA
Found at i:461153 original size:151 final size:150
Alignment explanation
Indices: 460898--461168 Score: 434
Period size: 151 Copynumber: 1.8 Consensus size: 150
460888 CAATTTAGAG
*
460898 TTTAGGGTTTGGGATGTAGGGTTTAAGGTTTATGGTATATTGGGGGTTAGATTTTGAGGTTTGCT
1 TTTAGGATTTGGGATGTAGGGTTTAAGGTTTATGGTATATTGGGGGTTAGATTTTGAGGTTTGCT
* *
460963 GGTTGGTGTTTATGGTTTACGGGCTTAATGTTTACAGTTTAGGGTTTACGATTTATAATTTATAG
66 GGTAGGTGTTTACGGTTTACGGGCTTAATGTTTACAGTTTAGGGTTTACGATTTATAATTTATAG
461028 TTTAGGGTTTAGGGTTAGTT
131 TTTAGGGTTTAGGGTTAGTT
* * * *
461048 TTTAGGATTTGGGATTTATGGTTTAAGGTTTATGGTATATTGGGGGGTTGGATTTTGAGGTTTGG
1 TTTAGGATTTGGGATGTAGGGTTTAAGGTTTATGGTATATT-GGGGGTTAGATTTTGAGGTTTGC
* * * *
461113 TGGTAGGTGTTTACGGTTTACGGGTTTATTGTTTATAGTTTAGGGTTTACGGTTTA
65 TGGTAGGTGTTTACGGTTTACGGGCTTAATGTTTACAGTTTAGGGTTTACGATTTA
461169 CGGGTTATAG
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
150 38 0.35
151 71 0.65
ACGTcount: A:0.18, C:0.03, G:0.33, T:0.46
Consensus pattern (150 bp):
TTTAGGATTTGGGATGTAGGGTTTAAGGTTTATGGTATATTGGGGGTTAGATTTTGAGGTTTGCT
GGTAGGTGTTTACGGTTTACGGGCTTAATGTTTACAGTTTAGGGTTTACGATTTATAATTTATAG
TTTAGGGTTTAGGGTTAGTT
Found at i:461167 original size:21 final size:22
Alignment explanation
Indices: 461128--461168 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
461118 GGTGTTTACG
**
461128 GTTTACGGGTTTATTGTTTATA
1 GTTTACGGGTTTACGGTTTATA
461150 GTTTA-GGGTTTACGGTTTA
1 GTTTACGGGTTTACGGTTTA
461169 CGGGTTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.17, C:0.05, G:0.27, T:0.51
Consensus pattern (22 bp):
GTTTACGGGTTTACGGTTTATA
Found at i:461454 original size:8 final size:8
Alignment explanation
Indices: 461437--461467 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
461427 TATATTTCTT
461437 AAAA-ATA
1 AAAATATA
461444 AAAATATA
1 AAAATATA
461452 AAAATATA
1 AAAATATA
461460 AAAATATA
1 AAAATATA
461468 TTGATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATATA
Found at i:462374 original size:6 final size:6
Alignment explanation
Indices: 462365--462396 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
462355 ATCTATTGCA
*
462365 TCACCA TCACCG TCACCG TCACCG TCACCG TC
1 TCACCG TCACCG TCACCG TCACCG TCACCG TC
462397 GCTCTCTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.50, G:0.12, T:0.19
Consensus pattern (6 bp):
TCACCG
Found at i:474738 original size:21 final size:21
Alignment explanation
Indices: 474712--474760 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
474702 ACAACTTAAT
* *
474712 GCAGAGGCGGCAGCGAGGGAA
1 GCAGAGGCGACAGCGAGAGAA
*
474733 GCAGAGGCTACAGCGAGAGAA
1 GCAGAGGCGACAGCGAGAGAA
474754 GCAGAGG
1 GCAGAGG
474761 TTCAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.47, T:0.02
Consensus pattern (21 bp):
GCAGAGGCGACAGCGAGAGAA
Found at i:475217 original size:42 final size:42
Alignment explanation
Indices: 475163--475329 Score: 228
Period size: 42 Copynumber: 3.9 Consensus size: 42
475153 TTGTGAAGAA
* *
475163 AGCGCCGCTAAAGAACATGATCTTCAGCGGCGTTTTTTTCTG
1 AGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTG
* *
475205 GGCGCCGCTAAAGAACATAATCTTTAGCGGTGTTTTTTT-TG
1 AGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTG
*
475246 TAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTA
1 --AGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTG
* * *
475290 AACGCCGCTAAAGAACATGACCTTTAGCGGCGTTTATTTT
1 AGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTT-TTTT
475330 TGTAAACACT
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.02
42 67 0.60
43 41 0.37
44 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
AGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTG
Found at i:475251 original size:85 final size:86
Alignment explanation
Indices: 475162--475334 Score: 267
Period size: 85 Copynumber: 2.0 Consensus size: 86
475152 TTTGTGAAGA
* *** *
475162 AAGCGCCGCTAAAGAACATGATCTTCAGCGGCGTTTTTTTCTGGGCGCCGCTAAAGAACATAATC
1 AAGCGCCGCTAAAGAACATAATCTTCAGCGGCGTTTTTTTCTAAACGCCGCTAAAGAACATAACC
*
475227 TTTAGCGGTGTTT-TTTTTGT
66 TTTAGCGGCGTTTATTTTTGT
* *
475247 AAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTAAACGCCGCTAAAGAACATGACC
1 AAGCGCCGCTAAAGAACATAATCTTCAGCGGCGTTTTTTTCTAAACGCCGCTAAAGAACATAACC
475312 TTTAGCGGCGTTTATTTTTGT
66 TTTAGCGGCGTTTATTTTTGT
475333 AA
1 AA
475335 ACACTGCAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 70 0.89
86 9 0.11
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (86 bp):
AAGCGCCGCTAAAGAACATAATCTTCAGCGGCGTTTTTTTCTAAACGCCGCTAAAGAACATAACC
TTTAGCGGCGTTTATTTTTGT
Found at i:475478 original size:22 final size:22
Alignment explanation
Indices: 475425--475476 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
475415 GCTAAAAAGT
475425 GCCGCTAAAGGCCTTAAAAAAC
1 GCCGCTAAAGGCCTTAAAAAAC
475447 GCCGCTAAAGGCCTT-AAAAAC
1 GCCGCTAAAGGCCTTAAAAAAC
475468 GCCGCTAAA
1 GCCGCTAAA
475477 AGCTTGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.38, C:0.29, G:0.19, T:0.13
Consensus pattern (22 bp):
GCCGCTAAAGGCCTTAAAAAAC
Found at i:477102 original size:15 final size:16
Alignment explanation
Indices: 477072--477108 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
477062 ACCCACCCAT
*
477072 ACCCAATCCAATATAA
1 ACCCAATACAATATAA
477088 ACCCAATAC-ATATAA
1 ACCCAATACAATATAA
477103 ACCCAA
1 ACCCAA
477109 GTACCTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.16
Consensus pattern (16 bp):
ACCCAATACAATATAA
Found at i:477177 original size:6 final size:6
Alignment explanation
Indices: 477168--477205 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
477158 AATAACAATC
477168 CTAAAA CTAAAA CTAAAA CTAAAA GTCTAAAA CTAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA --CTAAAA CTAAAA
477206 ATCACGACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 24 0.80
8 6 0.20
ACGTcount: A:0.63, C:0.16, G:0.03, T:0.18
Consensus pattern (6 bp):
CTAAAA
Found at i:478465 original size:12 final size:12
Alignment explanation
Indices: 478428--478478 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
478418 TATCATAGTT
478428 CTTACTT-CTT-
1 CTTACTTGCTTA
* *
478438 CTTTACTTACTCA
1 C-TTACTTGCTTA
*
478451 CTTACTTGTTTA
1 CTTACTTGCTTA
478463 CTTACTTGCTTA
1 CTTACTTGCTTA
478475 CTTA
1 CTTA
478479 AATAACTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 25 0.76
13 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (12 bp):
CTTACTTGCTTA
Found at i:478850 original size:49 final size:49
Alignment explanation
Indices: 478718--478852 Score: 216
Period size: 49 Copynumber: 2.8 Consensus size: 49
478708 GATAATAACA
* * * * *
478718 TGCCAAAGCCATGTCCCAAACATGGCCTTACATGAGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
478767 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
*
478816 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGA
478853 GTTCTCATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
Found at i:481140 original size:27 final size:27
Alignment explanation
Indices: 481094--481206 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
481084 TTACACTATT
* **
481094 ATGACCAAAATACCTTCATATGGTAAA
1 ATGACCGAAATACCCCCATATGGTAAA
* * *
481121 ATAACCGAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATATGGTAAA
* * *
481148 ATGACCGAAATACCTCTATAAGGTAAA
1 ATGACCGAAATACCCCCATATGGTAAA
481175 ATGACC-AACATACCCCCAT-TGGGTAAA
1 ATGACCGAA-ATACCCCCATAT-GGTAAA
481202 ATGAC
1 ATGAC
481207 TGTTATACCC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.03
27 68 0.97
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATATGGTAAA
Found at i:481173 original size:54 final size:54
Alignment explanation
Indices: 481094--481206 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 54
481084 TTACACTATT
* *
481094 ATGACCAAAATACCTTCATATGGTAAAATAACCGAA-ATACCCCCATAGGGTAGA
1 ATGACCAAAATACCTTCATAAGGTAAAATAACC-AACATACCCCCATAGGGTAAA
* * *
481148 ATGACCGAAATACC-TCTATAAGGTAAAATGACCAACATACCCCCATTGGGTAAA
1 ATGACCAAAATACCTTC-ATAAGGTAAAATAACCAACATACCCCCATAGGGTAAA
481202 ATGAC
1 ATGAC
481207 TGTTATACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
53 4 0.08
54 48 0.92
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (54 bp):
ATGACCAAAATACCTTCATAAGGTAAAATAACCAACATACCCCCATAGGGTAAA
Found at i:485886 original size:21 final size:21
Alignment explanation
Indices: 485861--485900 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
485851 TATAATTACT
485861 TCATG-CCAAAACATATATATA
1 TCATGACCAAAAC-TATATATA
485882 TCATGACCAAAACTATATA
1 TCATGACCAAAACTATATA
485901 ACTCAAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (21 bp):
TCATGACCAAAACTATATATA
Found at i:489815 original size:17 final size:17
Alignment explanation
Indices: 489793--489829 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
489783 GTAGTGATTC
*
489793 AATACTTTAATTCAATT
1 AATACTTTAACTCAATT
*
489810 AATACTTTAACTCAGTT
1 AATACTTTAACTCAATT
489827 AAT
1 AAT
489830 TTTTATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (17 bp):
AATACTTTAACTCAATT
Found at i:490085 original size:26 final size:26
Alignment explanation
Indices: 490056--490107 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
490046 ATATATAAAT
490056 TTAAAATTTTACAAAACCTTTGAGGG
1 TTAAAATTTTACAAAACCTTTGAGGG
490082 TTAAAATTTTACAAAACCTTTGAGGG
1 TTAAAATTTTACAAAACCTTTGAGGG
490108 GTTCTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (26 bp):
TTAAAATTTTACAAAACCTTTGAGGG
Found at i:490999 original size:27 final size:27
Alignment explanation
Indices: 490969--491054 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 27
490959 GAAACCAATA
* *
490969 TAGTCTGCTGGAACAGTAAACACGAGG
1 TAGTCCGCTGGAACAATAAACACGAGG
** *
490996 TAGTCCGCCAGTACAATAAACACGAGG
1 TAGTCCGCTGGAACAATAAACACGAGG
* * * *
491023 TAGTCCACTGGGATAATAAACACGGGG
1 TAGTCCGCTGGAACAATAAACACGAGG
491050 TAGTC
1 TAGTC
491055 TGTTAGGACA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.19
Consensus pattern (27 bp):
TAGTCCGCTGGAACAATAAACACGAGG
Found at i:500401 original size:22 final size:23
Alignment explanation
Indices: 500334--500435 Score: 86
Period size: 22 Copynumber: 4.5 Consensus size: 23
500324 AGTGAACAGG
* * *
500334 AAATATTCTCTAGCGTGAACAGT
1 AAATATTCTCTGGCATGAATAGT
** *
500357 AGAA-A-TCTCTGGCAAAAACAGT
1 A-AATATTCTCTGGCATGAATAGT
500379 AAGAT-TT-TCTGGCATGAATAGT
1 AA-ATATTCTCTGGCATGAATAGT
*
500401 AAATATTCTCTGGCATGACTAGT
1 AAATATTCTCTGGCATGAATAGT
*
500424 GAATATTCTCTG
1 AAATATTCTCTG
500436 TAGTTTGTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 3 0.05
22 31 0.48
23 28 0.44
24 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (23 bp):
AAATATTCTCTGGCATGAATAGT
Found at i:500414 original size:23 final size:23
Alignment explanation
Indices: 500326--500435 Score: 95
Period size: 23 Copynumber: 4.9 Consensus size: 23
500316 GAAAGACGAG
* * *
500326 TGAACAGGAAATATTCTCTAGCG
1 TGAACAGTAAATATTCTCTGGCA
500349 TGAACAGTAGAA-A-TCTCTGGCA
1 TGAACAGTA-AATATTCTCTGGCA
**
500371 AAAACAGTAAGAT-TT-TCTGGCA
1 TGAACAGTAA-ATATTCTCTGGCA
*
500393 TGAATAGTAAATATTCTCTGGCA
1 TGAACAGTAAATATTCTCTGGCA
*
500416 TG-ACTAGTGAATATTCTCTG
1 TGAAC-AGTAAATATTCTCTG
500436 TAGTTTGTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
21 3 0.04
22 32 0.46
23 33 0.47
24 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (23 bp):
TGAACAGTAAATATTCTCTGGCA
Found at i:503899 original size:38 final size:38
Alignment explanation
Indices: 503847--503919 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
503837 GGTGGGGGAA
* *
503847 TGTTGGAGTGATTTTAGGAGGAAAATATGGGATTGGAG
1 TGTTGGAGTAATTTTAGGAGGAAAATATAGGATTGGAG
*
503885 TGTTGGAGTAATTTTAGGAGGAGAATATAGGATTG
1 TGTTGGAGTAATTTTAGGAGGAAAATATAGGATTG
503920 TGGAGTTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (38 bp):
TGTTGGAGTAATTTTAGGAGGAAAATATAGGATTGGAG
Found at i:505458 original size:34 final size:34
Alignment explanation
Indices: 505420--505487 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
505410 CTCTAATGCT
*
505420 TACTGATACTGAAATGGACTTAGGCCTAAACTGA
1 TACTGATACTGAAAAGGACTTAGGCCTAAACTGA
* *
505454 TACTGATATTGAAAAGGGCTTAGGCCTAAACTGA
1 TACTGATACTGAAAAGGACTTAGGCCTAAACTGA
505488 GATTATCTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (34 bp):
TACTGATACTGAAAAGGACTTAGGCCTAAACTGA
Found at i:507949 original size:2 final size:2
Alignment explanation
Indices: 507944--507969 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
507934 CTCGGAGTAC
507944 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
507970 TGGAAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:512301 original size:21 final size:21
Alignment explanation
Indices: 512267--512307 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
512257 ATATTTCTTT
*
512267 TAAATTTAATTATAAGATAAA
1 TAAATTTAATTATAAAATAAA
512288 TAAATATTAA-TATAAAATAA
1 TAAAT-TTAATTATAAAATAA
512308 TATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATTTAATTATAAAATAAA
Found at i:512859 original size:16 final size:16
Alignment explanation
Indices: 512838--512868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
512828 CCGAAATCAT
512838 AATTTAATCTAAATAA
1 AATTTAATCTAAATAA
*
512854 AATTTAATTTAAATA
1 AATTTAATCTAAATA
512869 TATTTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAATCTAAATAA
Found at i:518138 original size:20 final size:20
Alignment explanation
Indices: 518109--518162 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
518099 ATATTTTAAA
* * *
518109 TAAAATATAAAAATATTTTT
1 TAAAAAATAAAAATAATTAT
518129 TAAAAAATAAAAATAATTAT
1 TAAAAAATAAAAATAATTAT
*
518149 GAAAAATATAAAAA
1 TAAAAA-ATAAAAA
518163 CTCTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAAATAAAAATAATTAT
Done.