Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008313.1 Hibiscus syriacus cultivar Beakdansim tig00111007_pilon, whole genome shotgun sequence
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: 115678
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2238 original size:31 final size:31
Alignment explanation
Indices: 2200--2353 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
2190 GGGTCGAGGG
2200 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
2231 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
2262 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
2293 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
2324 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
2354 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:11121 original size:28 final size:28
Alignment explanation
Indices: 11062--11121 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
11052 TTCCTTCAGT
* *
11062 CTCAAGAAAATCACTTAAAGTTGCAAAT
1 CTCAAGAAAATCACATAAAGTTGCAAAC
*
11090 CTCAAGAAAATCACATAAAGTTGCTAAC
1 CTCAAGAAAATCACATAAAGTTGCAAAC
11118 CTCA
1 CTCA
11122 GTCAAACCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (28 bp):
CTCAAGAAAATCACATAAAGTTGCAAAC
Found at i:11399 original size:16 final size:17
Alignment explanation
Indices: 11368--11400 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11358 ATGCAATCTT
*
11368 CATGAACATGTTATATA
1 CATGAACATGTGATATA
11385 CATGAA-ATGTGATATA
1 CATGAACATGTGATATA
11401 GAAACACGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (17 bp):
CATGAACATGTGATATA
Found at i:18539 original size:16 final size:17
Alignment explanation
Indices: 18518--18569 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
18508 TTTTTAATTT
18518 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
18534 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
18549 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
18566 AATT
1 AATT
18570 TAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:20937 original size:24 final size:24
Alignment explanation
Indices: 20890--20940 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
20880 TAAACACATG
*
20890 AATATAATTAAAATTATGCTATAT
1 AATATAATTAAAATTATGATATAT
20914 AATATAATTAAAATTAT-ATAATAT
1 AATATAATTAAAATTATGAT-ATAT
20938 AAT
1 AAT
20941 TTGTGGTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AATATAATTAAAATTATGATATAT
Found at i:21627 original size:84 final size:83
Alignment explanation
Indices: 21511--22581 Score: 1046
Period size: 84 Copynumber: 13.0 Consensus size: 83
21501 GCTATGTTGT
* *
21511 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC-TCA
1 AAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTC-
* * *
21575 TAGCCTTGAGTTATGCTGT
65 TAGACTTAAGTTATGCTGC
* * * * * * *
21594 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TT--TGGCAGATAGCTCTTC
1 AAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTC
* * *
21656 TCGACTTAAGCTATGCTAC
65 TAGACTTAAGTTATGCTGC
* * *
21675 AAATGATGTGCCGTTGAGCTAAGCGTAGTCGAACTCAAAGGTCTTT--T----G-----CCTTCT
1 AAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCT
* * *
21729 AGCCTTGAGTTATGCTGT
66 AGACTTAAGTTATGCTGC
* * * * ** *
21747 AAATGAAGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTTGGCAGACAACCCTT
1 AAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTT
* *
21812 ATAGACTTAAGTTGTGCTGC
64 CTAGACTTAAGTTATGCTGC
* * * * * * *
21832 AAATGATATGCCGTTGAGCCGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTC
* *
21897 TAGACTTAAGTTGTGTTGC
65 TAGACTTAAGTTATGCTGC
*
21916 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTT
*
21980 CTCGACTTAAGTTATGCTGC
64 CTAGACTTAAGTTATGCTGC
* * * ** *
22000 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT--TGGCAGATAGCCCTTC
1 AAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTC
* * *
22062 TCGACTTAAGCTATACTGC
65 TAGACTTAAGTTATGCTGC
* * * *
22081 AAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTC
* *
22146 TAGACTTAAGTTGTACTGC
65 TAGACTTAAGTTATGCTGC
*
22165 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTT
*
22229 CTCGACTTAAGTTATGCTGC
64 CTAGACTTAAGTTATGCTGC
* * * ** *
22249 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT--TGGCAGATAGCCCTTC
1 AAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTC
* * *
22311 TCGACTTAAGCTATACTGC
65 TAGACTTAAGTTATGCTGC
* * * * *
22330 AAATGATGTGCCGTTGAGCTGAGCATAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTC
*
22395 TAGACTTAAGTTGTGCTGC
65 TAGACTTAAGTTATGCTGC
* *
22414 AAATGATATG-CCTTGGAGCTGAGCGTATTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTT
*
22478 CTCGACTTAAGTTATGCTGC
64 CTAGACTTAAGTTATGCTGC
* * * * **
22498 AAATGATGTGCCCTCGAGGCTGAGTGTAATCGAACTCG-GGGTC-TT--TGGCAGATAGTCCTTC
1 AAATGATGTGCCCTTGA-GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTC
* *
22559 TTGACTTAAGCTATGCTGC
65 TAGACTTAAGTTATGCTGC
22578 AAAT
1 AAAT
22582 AGTTTGTTTG
Statistics
Matches: 816, Mismatches: 135, Indels: 77
0.79 0.13 0.07
Matches are distributed among these distances:
72 30 0.04
73 24 0.03
76 1 0.00
77 1 0.00
80 101 0.12
81 131 0.16
82 6 0.01
83 38 0.05
84 376 0.46
85 108 0.13
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (83 bp):
AAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCT
AGACTTAAGTTATGCTGC
Found at i:22118 original size:249 final size:249
Alignment explanation
Indices: 21736--22581 Score: 1469
Period size: 249 Copynumber: 3.4 Consensus size: 249
21726 TCTAGCCTTG
* *
21736 AGTTATGCTGTAAATGAAGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTTGGC
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGC
* * * * * * * * * *
21801 AGACAACCCTTATAGACTTAAGTTGTGCTGCAAATGATATGCCGTTGAGCCGAGTGTAGTCGAAC
62 AGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAAC
*
21866 TCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTG
127 TCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTG
21931 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
192 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
21989 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
22054 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
66 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
*
22119 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
131 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGC
22184 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
196 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
22238 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
*
22303 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTCGAACTCAA
66 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
22368 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGC
131 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGC
*
22433 TGAGCGTATTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
196 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
*
22487 AGTTATGCTGCAAATGATGTGCCCTCGAGGCTGAGTGTAATCGAACTC-GGGGTCTTTGGCAGAT
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
* * *
22551 AGTCCTTCTTGACTTAAGCTATGCTGCAAAT
66 AGCCCTTCTCGACTTAAGCTATACTGCAAAT
22582 AGTTTGTTTG
Statistics
Matches: 572, Mismatches: 21, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
248 44 0.08
249 474 0.83
251 1 0.00
253 53 0.09
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (249 bp):
AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGAT
AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAA
AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGC
TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
Found at i:22159 original size:333 final size:327
Alignment explanation
Indices: 21511--22581 Score: 1247
Period size: 333 Copynumber: 3.3 Consensus size: 327
21501 GCTATGTTGT
* * *
21511 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCC-TC
1 AAATGATATGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC
* * *
21574 ATAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
65 -TAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
* * *
21639 TTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCGTTGAGCTAAGCGTAGT
129 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGT
* * * *
21704 CGAACTCAAAGGTCTTT------T-G-CCTTCTAGCCTTGAGTTATGCTGTAAATGAAGTGCCCT
194 CGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCT
* * ** *
21761 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTTGGCAGACAACCCTTATAGACTTAAGTTG
258 TG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTG
21826 TGCTGC
322 TGCTGC
* * * *
21832 AAATGATATGCCGTTGAGCCGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATATGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC
* * * * * * *
21897 TAGACTTAAGTTGTGTTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
65 TAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--
* * * * *
21961 TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
128 T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCG
* *** * * *
22026 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
190 TAGTCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
22091 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAG
255 CC-TTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAG
*
22156 TTGTACTGC
319 TTGTGCTGC
*
22165 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATATGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC
* * *
22230 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
65 TAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTT
* *
22295 TGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTC
130 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
* * * *
22360 GAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGC
195 GAACTCAAAGGTC---T-TTGGCAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
* * *
22425 CTTGGAGCTGAGCGTATTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
256 CTT-GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGT
*
22490 TATGCTGC
320 TGTGCTGC
* * * * * **
22498 AAATGATGTGCCCTCGAGGCTGAGTGTAATCGAACTCG-GGGTC---T-TTGGCAGATAGTCCTT
1 AAATGATATG-CCTTGA-GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT
* *
22558 CTTGACTTAAGCTATGCTGCAAAT
64 CTAGACTTAAGTTATGCTGCAAAT
22582 AGTTTGTTTG
Statistics
Matches: 629, Mismatches: 96, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
321 66 0.10
322 39 0.06
323 3 0.00
325 46 0.07
326 24 0.04
329 57 0.09
330 47 0.07
332 7 0.01
333 263 0.42
334 77 0.12
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (327 bp):
AAATGATATGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT
AGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT
GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
AACTCAAAGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGA
GCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCT
GC
Found at i:26022 original size:18 final size:19
Alignment explanation
Indices: 25981--26025 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
25971 AGTTAATGTG
25981 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
26000 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
26018 AATGCAAA
1 AATGCAAA
26026 ATATCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:29052 original size:24 final size:24
Alignment explanation
Indices: 29005--29055 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
28995 TAAACACATG
*
29005 AATATAATTAAAATTATGCTATAT
1 AATATAATTAAAATTATGATATAT
29029 AATATAATTAAAATTAT-ATAATAT
1 AATATAATTAAAATTATGAT-ATAT
29053 AAT
1 AAT
29056 TTGTGGTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AATATAATTAAAATTATGATATAT
Found at i:29688 original size:53 final size:53
Alignment explanation
Indices: 29608--29719 Score: 206
Period size: 53 Copynumber: 2.1 Consensus size: 53
29598 CCACGCTTCA
29608 AATAATTGAGTGAAAATGAAGAATTAAATGGACAATAAAGACAATTCCTTTTT
1 AATAATTGAGTGAAAATGAAGAATTAAATGGACAATAAAGACAATTCCTTTTT
* *
29661 AATAATTGAGTGAAAATGAAGAATTAAATGGACAATAAAGACGATTCTTTTTT
1 AATAATTGAGTGAAAATGAAGAATTAAATGGACAATAAAGACAATTCCTTTTT
29714 AATAAT
1 AATAAT
29720 AGAAAGTGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.31
Consensus pattern (53 bp):
AATAATTGAGTGAAAATGAAGAATTAAATGGACAATAAAGACAATTCCTTTTT
Found at i:30797 original size:60 final size:59
Alignment explanation
Indices: 30700--30880 Score: 172
Period size: 60 Copynumber: 3.0 Consensus size: 59
30690 TCATATGTTT
* * *
30700 CCAAATTATAATTCTCATTTTAAATT-GATCCTTAAACTTTTAAATATTTCAATTTCATCC
1 CCAAATTATGATT-TCATTCTAAATTAG-TCCTAAAACTTTTAAATATTTCAATTTCATCC
*
30760 CCAAATTATGTATTTCATTCTAAATTAGTCCTAAAACTTTTGAATA-TTCTAATTTCATCC
1 CCAAATTATG-ATTTCATTCTAAATTAGTCCTAAAACTTTTAAATATTTC-AATTTCATCC
* ** * ** *
30820 CTAAACCATGACCTTT-GTTCTAAATTAGTCCCCAAACTTTTCAAA-ATTTCAATTTTATCC
1 CCAAATTATGA--TTTCATTCTAAATTAGTCCTAAAACTTTT-AAATATTTCAATTTCATCC
30880 C
1 C
30881 TAAAGTCATC
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
59 4 0.04
60 86 0.84
61 12 0.12
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (59 bp):
CCAAATTATGATTTCATTCTAAATTAGTCCTAAAACTTTTAAATATTTCAATTTCATCC
Found at i:31974 original size:41 final size:39
Alignment explanation
Indices: 31917--32000 Score: 96
Period size: 41 Copynumber: 2.1 Consensus size: 39
31907 CAGGCTTATA
* * * *
31917 AGGCTTTTTAATAGGCCTAAGTCTGGCCTGTTTAATTAAAT
1 AGGCTTTTAAAAAGGCCTAA-CCTGGCAT-TTTAATTAAAT
* *
31958 AGGCTTTTAAAAAGGCCTGACCTGGCATTTTTATTAAAT
1 AGGCTTTTAAAAAGGCCTAACCTGGCATTTTAATTAAAT
31997 AGGC
1 AGGC
32001 CATGCCAGGC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 14 0.38
40 6 0.16
41 17 0.46
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (39 bp):
AGGCTTTTAAAAAGGCCTAACCTGGCATTTTAATTAAAT
Found at i:32032 original size:31 final size:30
Alignment explanation
Indices: 31997--32089 Score: 131
Period size: 31 Copynumber: 3.2 Consensus size: 30
31987 TTTATTAAAT
31997 AGGCCATGCCAGGCCAGGCTTTATACATGTC
1 AGGCCA-GCCAGGCCAGGCTTTATACATGTC
32028 AGGCCAGACCAGGCCAGGCTTTATACATGTC
1 AGGCCAG-CCAGGCCAGGCTTTATACATGTC
*
32059 AGGCCAG--A--CCAGGCTTTATACAGGTC
1 AGGCCAGCCAGGCCAGGCTTTATACATGTC
32085 AGGCC
1 AGGCC
32090 GTAGGCCCCT
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
26 22 0.37
28 1 0.02
30 1 0.02
31 36 0.60
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (30 bp):
AGGCCAGCCAGGCCAGGCTTTATACATGTC
Found at i:32034 original size:26 final size:26
Alignment explanation
Indices: 32004--32089 Score: 109
Period size: 26 Copynumber: 3.1 Consensus size: 26
31994 AATAGGCCAT
32004 GCCAGGCCAGGCTTTATACATGTCAGG
1 GCCAGGCCAGGCTTTATACATGTCA-G
32031 CCAGACCAGGCCAGGCTTTATACATGTCAG
1 ---G-CCAGGCCAGGCTTTATACATGTCAG
* *
32061 GCCAGACCAGGCTTTATACAGGTCAG
1 GCCAGGCCAGGCTTTATACATGTCAG
32087 GCC
1 GCC
32090 GTAGGCCCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
26 26 0.49
27 1 0.02
30 2 0.04
31 24 0.45
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (26 bp):
GCCAGGCCAGGCTTTATACATGTCAG
Found at i:32900 original size:2 final size:2
Alignment explanation
Indices: 32893--32941 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
32883 TGAGTTTTAT
32893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32935 TA TA TA T
1 TA TA TA T
32942 GAGTTACTCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34337 original size:23 final size:21
Alignment explanation
Indices: 34303--34347 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
34293 GATATAAAAA
34303 TTATTTTTTATTCAATGTTTTT
1 TTATTTTTTATTCAAT-TTTTT
*
34325 TTATATTTTTATTTAATTTTTT
1 TTAT-TTTTTATTCAATTTTTT
34347 T
1 T
34348 AAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTATTTTTTATTCAATTTTTT
Found at i:34728 original size:23 final size:23
Alignment explanation
Indices: 34702--34749 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
34692 ATAAAGTACA
*
34702 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
34725 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
34748 AT
1 AT
34750 TTACTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:35201 original size:23 final size:23
Alignment explanation
Indices: 35166--35238 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
35156 ATACTTTACA
*
35166 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
35189 ATATAAACGCTACCTATTACAAT
1 ATATAAGCGCTACCTATTACATT
*
35212 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
35235 ATAT
1 ATAT
35239 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:35618 original size:431 final size:430
Alignment explanation
Indices: 34816--36302 Score: 2742
Period size: 431 Copynumber: 3.5 Consensus size: 430
34806 TATTACATTA
* *
34816 TATTATATTGAAACTGTCCATACTTTTTATAAAAAGGATCGATACTTCATTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
34881 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
34946 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
35011 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
35076 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
* *
35141 TTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTAT
326 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
*
35206 TACAATATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
35246 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
35311 TTATGTTTCAATTTTTTTTAAAAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
35376 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
35441 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
35506 CTTAAAACTAACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
35571 TTTATAAAAATGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
35636 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
35677 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
* * *
35742 TTATGTTTCAATTTTTTTTAATAGCGTTTCGTGTTTTCCACCTATAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* *
35807 AGTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
*
35872 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* * *
35937 CTTAAAACCCACTCAAATGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
*
36002 TTTATAAAAAGGATAGATACTTTACAATATAATCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
36067 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
36108 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
36173 TTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
* *
36238 TTTGCACAAAAAATTATTTTATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
36302 A
196 A
36303 CAACATTAAC
Statistics
Matches: 1025, Mismatches: 31, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
429 10 0.01
430 175 0.17
431 840 0.82
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:35633 original size:23 final size:23
Alignment explanation
Indices: 35607--35669 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
35597 ATATAACCAC
35607 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
35630 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
35653 TACCTATTACATCATAT
1 TACCTATTACATTATAT
35670 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:36064 original size:23 final size:23
Alignment explanation
Indices: 36038--36100 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
36028 ATATAATCAC
36038 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
36061 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
36084 TACCTATTACATCATAT
1 TACCTATTACATTATAT
36101 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:36575 original size:39 final size:39
Alignment explanation
Indices: 36521--36607 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
36511 TCAAGTTGTA
*
36521 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
36560 GATTTTGATTTCCTTTTGTTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
36599 GATTTTGAT
1 GATTTTGAT
36608 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:36900 original size:18 final size:18
Alignment explanation
Indices: 36877--36913 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36867 CGAAATATAT
36877 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
36895 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
36913 A
1 A
36914 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:37764 original size:25 final size:25
Alignment explanation
Indices: 37707--37772 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
37697 CACTCAAAAG
* *
37707 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGATA
***
37732 ACAAACATACCTAAATATGTAGATA
1 ATGTACATACCTAAATATGTAGATA
*
37757 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
37773 TTAATGATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGATA
Found at i:40548 original size:183 final size:182
Alignment explanation
Indices: 40240--40732 Score: 860
Period size: 183 Copynumber: 2.7 Consensus size: 182
40230 TTAAAATTAC
*
40240 CGACACTTTTTTAAATGGTATCGACATATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
40305 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
40370 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
40423 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGTACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
40488 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGAATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
40553 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
40606 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTA-AATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* * *
40671 ATTAAAATGTGTCGATTTAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCG
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
40733 ATAGCATTGT
Statistics
Matches: 295, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 292 0.99
184 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (182 bp):
CGACACTTTTTTAAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:41149 original size:23 final size:23
Alignment explanation
Indices: 41123--41185 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
41113 ATATAACCAC
41123 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
41146 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
41169 TACCTATTACATCATAT
1 TACCTATTACATTATAT
41186 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:41577 original size:23 final size:23
Alignment explanation
Indices: 41551--41613 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
41541 ATATAACCAC
41551 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
41574 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
41597 TACCTATTACATCATAT
1 TACCTATTACATTATAT
41614 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:42012 original size:23 final size:23
Alignment explanation
Indices: 41986--42044 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
41976 AACCACTACC
41986 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
42009 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
42032 TATTACATCATAT
1 TATTACATTATAT
42045 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:42168 original size:431 final size:431
Alignment explanation
Indices: 40769--42673 Score: 3463
Period size: 431 Copynumber: 4.4 Consensus size: 431
40759 TTATAATATG
* * *
40769 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATGCTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
40834 TCAATTTTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TCAATTTTTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
*
40898 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAATAAT
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAAT
*
40963 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAGATCTTAAA
195 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
41028 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATA
260 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATA
41093 AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
325 AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
41158 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
* *
41200 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
41265 TCAA--TTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TCAATTTTTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
*
41327 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAATAAT
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAAT
41392 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
195 AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAA
41457 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATAGACACTTTTATA
260 ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATA
41521 AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
325 AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACAT
41586 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
41628 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
*
41693 TCAATTTTTTTTAAAAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
41758 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
41823 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
196 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
* *
41888 CTAACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
261 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
* *
41953 AAATGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTACATT
326 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
42018 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
42059 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
* * * *
42124 TCAATTTTTTTTAATAGCGTTTCGTGTTTTCCACCTATAATATTAATTTAATAATTTCAGTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
42189 CAAAAAATTATTTGATTGTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAA-TT--TAATA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
*
42250 ATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATATCTTAAAA
196 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
* * * *
42315 CCCACTCAAATGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
261 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
42380 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
326 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
42445 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
42486 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
*
42551 TCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
42615 CAAAAAATTATTTTATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAA
42674 CAACATTAAC
Statistics
Matches: 1433, Mismatches: 33, Indels: 18
0.97 0.02 0.01
Matches are distributed among these distances:
426 91 0.06
427 318 0.22
428 196 0.14
429 232 0.16
430 246 0.17
431 350 0.24
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (431 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:42435 original size:23 final size:23
Alignment explanation
Indices: 42409--42471 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
42399 ATATAACCAC
42409 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
42432 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
42455 TACCTATTACATCATAT
1 TACCTATTACATTATAT
42472 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:42981 original size:2 final size:2
Alignment explanation
Indices: 42974--42998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42964 TGAGTTTTAT
42974 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42999 GAGTTACTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44716 original size:23 final size:23
Alignment explanation
Indices: 44690--44737 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
44680 ATAAAGTACA
*
44690 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
44713 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
44736 AT
1 AT
44738 TTACTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:45188 original size:23 final size:23
Alignment explanation
Indices: 45153--45225 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
45143 ATACTTTACA
*
45153 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
45176 ATATAAACGCTACCTATTACAAT
1 ATATAAGCGCTACCTATTACATT
*
45199 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
45222 ATAT
1 ATAT
45226 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:45605 original size:431 final size:430
Alignment explanation
Indices: 44804--46290 Score: 2699
Period size: 431 Copynumber: 3.5 Consensus size: 430
44794 TATTACATTA
* *
44804 TATTATATTGAAACTGTCCATACTTTTTATAAAAAGGATCGATACTTCATTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
44869 TTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
44933 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
44998 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
45063 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
* *
45128 TTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTAT
326 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
*
45193 TACAATATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
45233 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
45298 TTATGTTTCAATTTTTTTTAAAAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
45363 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
45428 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
45493 CTTAAAACTAACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
* *
45558 TTTATAAAAATGATAGATATTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
45623 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
45664 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
* * * *
45729 TTATGTATCAATTTTTTTTAATAGCGTTTCGTGTTTTCCACCTATAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* *
45794 AGTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
*
45859 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAATAT
195 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* * *
45924 CTTAAAACCCACTCAAATGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
45989 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
325 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
46054 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
* *
46095 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATATAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTT-AAAGTTATGTAA
*
46160 TTTATGTTTCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTC
65 TTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* *
46225 ATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
46289 AA
195 AA
46291 CAACATTAAC
Statistics
Matches: 1019, Mismatches: 36, Indels: 5
0.96 0.03 0.00
Matches are distributed among these distances:
429 74 0.07
430 10 0.01
431 913 0.90
432 22 0.02
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:45610 original size:23 final size:23
Alignment explanation
Indices: 45584--45656 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
45574 ATATTTTACA
45584 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
*
45607 ATATAAACGA-TACCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* * *
45630 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATT
45653 ATAT
1 ATAT
45657 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
22 2 0.05
23 37 0.86
24 4 0.09
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:46051 original size:23 final size:23
Alignment explanation
Indices: 46025--46087 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
46015 ATATAACCAC
46025 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
46048 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
46071 TACCTATTACATCATAT
1 TACCTATTACATTATAT
46088 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:47686 original size:6 final size:6
Alignment explanation
Indices: 47675--47737 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
47665 ACTTGTTTGG
* * * *
47675 ATCTTC ATCTTC ATCATC ATCATC ATCATC ATCGTCATC ATCTTC ATCGTC
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATC-T--TC ATCTTC ATCTTC
*
47726 AGCTTC ATCTTC
1 ATCTTC ATCTTC
47738 TGCGACCGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 42 0.88
8 1 0.02
9 5 0.10
ACGTcount: A:0.22, C:0.33, G:0.05, T:0.40
Consensus pattern (6 bp):
ATCTTC
Found at i:47693 original size:3 final size:3
Alignment explanation
Indices: 47679--47722 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
47669 GTTTGGATCT
* * *
47679 TCA TCT TCA TCA TCA TCA TCA TCA TCA TCG TCA TCA TCT TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
47723 GTCAGCTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:49541 original size:198 final size:199
Alignment explanation
Indices: 49203--49974 Score: 1458
Period size: 199 Copynumber: 3.9 Consensus size: 199
49193 TTTAAATTAG
49203 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
49267 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* *
49332 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
49397 AAAA
196 AAAA
* *
49401 TATCGACACCAACTAAAA-AGTGTCGACACATTAGTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
49465 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
49530 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
49595 AAAA
196 AAAA
*
49599 TATCGACACAAACTAAAATAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
49664 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
49729 CGACACTTTTTATATATGAATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
49794 AAAA
196 AAAA
49798 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
49863 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
49928 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
49975 GGCCATATTG
Statistics
Matches: 561, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
198 211 0.38
199 288 0.51
200 62 0.11
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:50139 original size:19 final size:19
Alignment explanation
Indices: 50093--50141 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
50083 TTATATACAC
*
50093 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
50112 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
50131 ATACAAAATTA
1 ATACAAAATTA
50142 ACCCTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:51887 original size:33 final size:33
Alignment explanation
Indices: 51850--51915 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
51840 CATCTTAATA
*
51850 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
51883 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
51916 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:51974 original size:21 final size:21
Alignment explanation
Indices: 51949--51992 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
51939 CCCCTTATGC
51949 CTCTCAAGTATATCTTCGACT
1 CTCTCAAGTATATCTTCGACT
* *
51970 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTATATCTTCGACT
51991 CT
1 CT
51993 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTATATCTTCGACT
Found at i:54245 original size:17 final size:18
Alignment explanation
Indices: 54223--54265 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
54213 ATATATCCGG
54223 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
54240 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
54260 TATCAT
1 TATCAT
54266 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:54428 original size:161 final size:162
Alignment explanation
Indices: 54251--54553 Score: 500
Period size: 161 Copynumber: 1.9 Consensus size: 162
54241 ATCATTTTGA
* * * *
54251 TACCGGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGCTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
*
54316 ACACATTATAGGCGGTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
66 ACACATTATAGGAGGTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
*
54380 TATCGACACTTTCAATATATCTGGTAACGTTT
131 TACCGACACTTTCAATATATCTGGTAACGTTT
*
54412 TACCGGCTTTATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
1 TACCGGCTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
* ** *
54477 ACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAG
66 ACACATTATAGGAGGTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
54542 TACCGACACTTT
131 TACCGACACTTT
54554 AAATGCATCC
Statistics
Matches: 130, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
161 114 0.88
162 16 0.12
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (162 bp):
TACCGGCTTTATCATATTTTTACATGGTATATCGTTGTGGATCGATACATTTTTTAAAAGTATCG
ACACATTATAGGAGGTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
TACCGACACTTTCAATATATCTGGTAACGTTT
Found at i:55168 original size:229 final size:228
Alignment explanation
Indices: 54718--55208 Score: 894
Period size: 229 Copynumber: 2.1 Consensus size: 228
54708 ACTTTTATAC
*
54718 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAATT
54783 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
*
54848 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAT
131 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
*
54913 ATAATAATAAATATGTTTTCCACAGTGAAATAA
196 ATAATAATAAATATATTTTCCACAGTGAAATAA
*
54946 GTATAGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAAAT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTC-AAAT
*
55011 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
65 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
*
55076 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
130 TTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
55141 AGATAATAATAAATATATTTT-CACAGTGAAATAA
194 AGATAATAATAAATATATTTTCCACAGTGAAATAA
*
55175 GTATGGACACTTTTATAAAAAGGATATATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
55209 ACAATATAAC
Statistics
Matches: 253, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
228 59 0.23
229 122 0.48
230 72 0.28
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (228 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAATT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
TATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATAAATATATTTTCCACAGTGAAATAA
Found at i:55471 original size:11 final size:11
Alignment explanation
Indices: 55455--55479 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55445 ATCCGGTACT
55455 ACCGTATATTA
1 ACCGTATATTA
55466 ACCGTATATTA
1 ACCGTATATTA
55477 ACC
1 ACC
55480 CGTCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:56245 original size:37 final size:37
Alignment explanation
Indices: 56172--56246 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
56162 GTTGGAAAAT
*
56172 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
56209 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
56246 A
1 A
56247 AGGTTTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:57272 original size:656 final size:656
Alignment explanation
Indices: 55961--57261 Score: 2027
Period size: 656 Copynumber: 2.0 Consensus size: 656
55951 TTATCCTAAA
* * *
55961 GGTGCGTTTAGTTCACGGAATGTAAGATTATCAGTAGGAATAAAAGATTACCAGGGAATAGGATT
1 GGTGCGTTTAGTTCACGGAATGTAAGATTACCAGTAGAAATAAAAGATTACCAGGGAATACGATT
* **
56026 ACTGAGAATATTGTATTTTGTGTTTGGTTGGTTTGGCAGGAATGTAAGATTACCGTGTTTGATTA
66 ACTGAGAATATTGTATTTTGTGTTTGGTTGGCTTAACAGGAATGTAAGATTACCGTGTTTGATTA
*
56091 AAGGAATAAAAAATTATTGGAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTTTT
131 AAGGAATAAAAAATTACTGGAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTTTT
*
56156 TAACAAGTTGGAAAATATTTATATATTTTCTTTAAAAAAATTAAATTCATAAAATTTATATAATT
196 TAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAAATTAAATTCATAAAATTTATATAATT
*
56221 TTTTTTACAAAATTGAAAATATAAAAAGGTTTAAGGAAAGGGTAAAATTTTATTTTAACCCCTGA
261 TTGTTTACAAAATTGAAAATATAAAAAGGTTTAAGGAAAGGGTAAAATTTTATTTTAACCCCTGA
*
56286 ACTTCATATAAAATTTTAATTATATATTTTTTTATAAATCTAAAATAGTTTAAGGATAAATTTAT
326 ACTTCATATAAAATTTTAATTATAGATTTTTTTATAAATCTAAAATAGTTTAAGGATAAATTTAT
56351 AATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAATAAAGATATTTTTGAAAAAAAATTA
391 AATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAATAAAGATATTTTTGAAAAAAAATTA
* * *** * * *
56416 AGGGCATTTTAGTCTAAAATGTTGGTAATCCAACAATACCTAAAGAAAGGGAGGTAATTACATTC
456 AGGGCATTTTAGTCCAAAACGCCAGTAATCCAACAATACATAAAGAAAGGGAAGTAATGACATTC
* * * *
56481 CCGGTAATATACCCCAAAAAATCCACTATTGGTAATGTAAGATTACCGGGAATGACATTCCCGAC
521 CCGATAATATACCCCAAAAAATCCACTATTGGTAATCTAAGATTACCGAGAATGACATTCCAGAC
* * * * * *
56546 CAACCAAACGGGAGAATGTGGATTCGATTTCTATGGGAATCTCACATTCCCCCAACCAAACCCAC
586 CAACCAAACGGGAGAATGTAGATTCCATTCCCATAGGAATCCCACATTCCCCCAACCAAACCCAC
56611 CCTTAG
651 CCTTAG
* ** *
56617 GGTGCGTTTGGTTCACAGG-ATGTAAGATTACCAGT-GAAAATGTAAGATTATCAGGGAATACGA
1 GGTGCGTTTAGTTCAC-GGAATGTAAGATTACCAGTAG-AAATAAAAGATTACCAGGGAATACGA
* * *
56680 TTACTGAGAATGTTGTATTTTGTGTTTGGTTGGCTTAACAGGAATGTAAGATTACTGTGTTTGGT
64 TTACTGAGAATATTGTATTTTGTGTTTGGTTGGCTTAACAGGAATGTAAGATTACCGTGTTTGAT
* *
56745 TAAATGAATAAAAGATTACTGGAATGTATATTTGACCAAATTGTCCTTATTATATATTTA-TTTT
129 TAAAGGAATAAAAAATTACTGGAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTT
*
56809 TTTAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATATAA
194 TTTAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAAATTAAATTCATAAAATTTATATAA
*
56874 -TTTGTTTACAAAATTGAAAATATAAAAAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCCT
259 TTTTGTTTACAAAATTGAAAATATAAAAAGGTTTAAGGAAAGGGTAAAATTTTATTTTAACCCCT
* *
56938 GAATTTCATATAAAATTTTAATTATAGACTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATT
324 GAACTTCATATAAAATTTTAATTATAGA-TTTTTTTATAAATCTAAAATAGTTTAAGGATAAATT
* * * *
57003 TGTAATTTAACCTTCGTAGGATTTTTATTATTCAATGACAGAATAATGATATTTTTGAAAAAAAA
388 TATAATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAATAAAGATATTTTTG-AAAAAAA
*
57068 ATTAAGGGCATTTTAGTCCAAAACGCCAGTAATTCAACAATACATAAAGAAAGGGAAGTAATGAC
452 ATTAAGGGCATTTTAGTCCAAAACGCCAGTAATCCAACAATACATAAAGAAAGGGAAGTAATGAC
* * *
57133 ATTCCCGATAATATA-CCCAAAAAATCCACTATTGGTAATCTTATATTACCGAGAATGAGATTTC
517 ATTCCCGATAATATACCCCAAAAAATCCACTATTGGTAATCTAAGATTACCGAGAATGACA-TTC
*** * * *
57197 CAGGGTAACCAAACGGGGGAATGTAGCTTCCATTCCCATAGGAATCCCACATTCCCCCATCCAAA
581 CAGACCAACCAAACGGGAGAATGTAGATTCCATTCCCATAGGAATCCCACATTCCCCCAACCAAA
57262 TGCCCCCTTA
Statistics
Matches: 585, Mismatches: 55, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
654 88 0.15
655 196 0.34
656 299 0.51
657 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (656 bp):
GGTGCGTTTAGTTCACGGAATGTAAGATTACCAGTAGAAATAAAAGATTACCAGGGAATACGATT
ACTGAGAATATTGTATTTTGTGTTTGGTTGGCTTAACAGGAATGTAAGATTACCGTGTTTGATTA
AAGGAATAAAAAATTACTGGAATGTATATTTGACCAAATTGTCCTTATTATATATTTATTTTTTT
TAACAAGTTGAAAAATATTTATATATTTTCTTTAAAAAAATTAAATTCATAAAATTTATATAATT
TTGTTTACAAAATTGAAAATATAAAAAGGTTTAAGGAAAGGGTAAAATTTTATTTTAACCCCTGA
ACTTCATATAAAATTTTAATTATAGATTTTTTTATAAATCTAAAATAGTTTAAGGATAAATTTAT
AATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAATAAAGATATTTTTGAAAAAAAATTA
AGGGCATTTTAGTCCAAAACGCCAGTAATCCAACAATACATAAAGAAAGGGAAGTAATGACATTC
CCGATAATATACCCCAAAAAATCCACTATTGGTAATCTAAGATTACCGAGAATGACATTCCAGAC
CAACCAAACGGGAGAATGTAGATTCCATTCCCATAGGAATCCCACATTCCCCCAACCAAACCCAC
CCTTAG
Found at i:57627 original size:20 final size:20
Alignment explanation
Indices: 57599--57639 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
57589 CTAAATTAGG
*
57599 TATTATTATTTATTTACATT
1 TATTATTATATATTTACATT
* *
57619 TATTCTTATATATTTATATT
1 TATTATTATATATTTACATT
57639 T
1 T
57640 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTATATATTTACATT
Found at i:61444 original size:22 final size:22
Alignment explanation
Indices: 61419--61462 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
61409 TATATTACAA
61419 TTATAATAT-ATTAAAATTATTT
1 TTAT-ATATCATTAAAATTATTT
* *
61441 TTATTTTTCATTAAAATTATTT
1 TTATATATCATTAAAATTATTT
61463 AAAATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATCATTAAAATTATTT
Found at i:62149 original size:22 final size:22
Alignment explanation
Indices: 62085--62167 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
62075 TTTTATAAAT
* *
62085 ATTATAT-TTTAATTAAATTACA
1 ATTATATGTTTAA-TAATTTATA
* * *
62107 TTTATATTTTTAAATAGTTTATA
1 ATTATATGTTT-AATAATTTATA
62130 ATTATATGTTTAATAATTTATA
1 ATTATATGTTTAATAATTTATA
*
62152 ATT-TAATGTTTTATAA
1 ATTAT-ATGTTTAATAA
62168 ATTAATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 29 0.58
23 18 0.36
24 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTATATGTTTAATAATTTATA
Found at i:75224 original size:45 final size:45
Alignment explanation
Indices: 75164--75253 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
75154 AGTTAACCAC
75164 CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
1 CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
*
75209 CTTACAGATAGGTCTAACTATATACAGCATGAAATGCCAAATTAA
1 CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
75254 GAGAACGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (45 bp):
CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
Found at i:77422 original size:224 final size:218
Alignment explanation
Indices: 77022--77460 Score: 639
Period size: 224 Copynumber: 2.0 Consensus size: 218
77012 TTGGAAACTG
* *
77022 CATTATGTTTCTCCAACAAGATAAAACGTAATTGCAGCCTTCTATGATCTATCAAGACAGATGGT
1 CATTATGTTTCTCCAACAAGATAAAACATAATTGCAGCCTTCTACGATCTATCAAGACAGATGGT
77087 TCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAACCAAA
66 TCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAACCAAA
* ** * * * *
77152 AGCTTCATTCATGGGTTGTAAACTTCAAATTGACCCCAGATTAACTACCTTATTTAGGGGGCAGC
131 AACTTCATTCATGGGCCGTAAACTTCAAATGGACCCAAGATTAACTA--TTATTGA-GGGGCAGA
*
77217 ATTTTTACCTAAAGTAGCATTAGCTA
193 ATTTCTACCTAAAGTAGCATTAGCTA
*
77243 CATTATCG-TTCTGCAACAAGATAAAACATAATTGCAGCCTTCTACGATCTACTATCAAAGACAG
1 CATTAT-GTTTCTCCAACAAGATAAAACATAATTGCAGCCTTCTACGA--T-CTATC-AAGACAG
* * * * *
77307 ATGGTTCCAGGAATTTTGCCGAATAGGTCAAAAGGGTA-GATGTATGTTAACATGTAGGTAGTAA
61 ATGGTTCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAA
*
77371 CCAAAAACTTCATTCGTGGGCCGTAAACTTCAAATGGACCCAAGATTAACTATTATTGAGGGGCA
126 CCAAAAACTTCATTCATGGGCCGTAAACTTCAAATGGACCCAAGATTAACTATTATTGAGGGGCA
77436 GAATTTCTACCTAAAGTAGCATTAG
191 GAATTTCTACCTAAAGTAGCATTAG
77461 TTATATTCAA
Statistics
Matches: 196, Mismatches: 17, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
221 71 0.36
222 7 0.04
223 1 0.01
224 74 0.38
225 43 0.22
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (218 bp):
CATTATGTTTCTCCAACAAGATAAAACATAATTGCAGCCTTCTACGATCTATCAAGACAGATGGT
TCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAACCAAA
AACTTCATTCATGGGCCGTAAACTTCAAATGGACCCAAGATTAACTATTATTGAGGGGCAGAATT
TCTACCTAAAGTAGCATTAGCTA
Found at i:81618 original size:29 final size:30
Alignment explanation
Indices: 81549--81618 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
81539 CAGAGCGATC
* *
81549 AAAATATGAATAATTCAAAAGTTATGTGAA
1 AAAATATGAAAAATTCAAAAGTTAAGTGAA
81579 AAAAT-TAGAAAAATT-AAAAG-TACAGTGAA
1 AAAATAT-GAAAAATTCAAAAGTTA-AGTGAA
*
81608 TAAATATGAAA
1 AAAATATGAAA
81619 GAGAGTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.06
29 19 0.56
30 13 0.38
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (30 bp):
AAAATATGAAAAATTCAAAAGTTAAGTGAA
Found at i:96365 original size:13 final size:13
Alignment explanation
Indices: 96347--96371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
96337 CAATATTTTG
96347 AATAATTTCAGAC
1 AATAATTTCAGAC
96360 AATAATTTCAGA
1 AATAATTTCAGA
96372 GCAAATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
AATAATTTCAGAC
Found at i:99380 original size:51 final size:51
Alignment explanation
Indices: 99321--99422 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
99311 GCCTTTGACA
99321 ACCAACTGAGAGACCAATGTATCAAGAGACTCGCTTTGATAAAGTTGAAAT
1 ACCAACTGAGAGACCAATGTATCAAGAGACTCGCTTTGATAAAGTTGAAAT
99372 ACCAACTGAGAGACCAATGTATCAAGAGACTCGCTTTGATAAAGTTGAAAT
1 ACCAACTGAGAGACCAATGTATCAAGAGACTCGCTTTGATAAAGTTGAAAT
99423 TGATACTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (51 bp):
ACCAACTGAGAGACCAATGTATCAAGAGACTCGCTTTGATAAAGTTGAAAT
Found at i:102380 original size:26 final size:27
Alignment explanation
Indices: 102334--102384 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
102324 AATAATAATA
102334 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
102362 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
102385 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:102521 original size:35 final size:38
Alignment explanation
Indices: 102399--102734 Score: 158
Period size: 37 Copynumber: 8.8 Consensus size: 38
102389 TTTTTTAAAA
102399 AAAACTATATATTATATAT-ATTTTC-AAAATGGTTTT-
1 AAAACTATATATTATATATAATTTTCAAAAAT-GTTTTC
* *
102435 -----TATATATTATATA-AATGTTTTC-ATAACGTTTTC
1 AAAACTATATATTATATATAA--TTTTCAAAAATGTTTTC
*
102468 AAAAGTATATATTATATAT-ATTTT-AAAAATGTTTTC
1 AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
*
102504 AAAAACTATATA-T-TATATAATTTTCAAAAAATATATTTTC
1 -AAAACTATATATTATATATAATTTTC--AAAA-ATGTTTTC
* * * * *
102544 AAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTC-ATAACGTTTTC
1 AAAA------CT--ATA-TAT-TA-TATAT-AATTTT--CAAAAATGTTTTC
* *
102595 AAAAGTATATATTATATAT-ATTTT-AAAAACGTTTTC
1 AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
* *
102631 AAAAACTATATA-T-TATATAATTTTCAAAAATATTTTA
1 -AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
* *
102668 AAAACTATATAATATACAT-ATTTTCAAAAATGTTTT-
1 AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
* *
102704 -AAACTATATACTATATATGTATTTTCAAAAA
1 AAAACTATATATTATATAT-AATTTTCAAAAA
102735 CAATTTGCAA
Statistics
Matches: 235, Mismatches: 24, Indels: 81
0.69 0.07 0.24
Matches are distributed among these distances:
31 14 0.06
32 5 0.02
33 8 0.03
35 26 0.11
36 46 0.20
37 57 0.24
38 22 0.09
39 8 0.03
40 12 0.05
41 2 0.01
42 3 0.01
43 2 0.01
45 2 0.01
47 2 0.01
48 2 0.01
50 1 0.00
51 10 0.04
52 7 0.03
53 5 0.02
55 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
Found at i:102531 original size:25 final size:25
Alignment explanation
Indices: 102499--102575 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
102489 TTTAAAAATG
*
102499 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
102524 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
102551 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
102576 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:102543 original size:15 final size:16
Alignment explanation
Indices: 102518--102547 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
102508 ACTATATATT
102518 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
102534 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
102548 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:102582 original size:27 final size:26
Alignment explanation
Indices: 102481--102582 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
102471 AGTATATATT
* *
102481 ATATATATTTTAAAAATGTTTTCAAAA
1 ATATATATTATATAAATGTTTT-AAAA
*
102508 ACTATATATTATAT-AAT-TTTCAAAA
1 A-TATATATTATATAAATGTTTTAAAA
*
102533 A-ATATATTTTCA-AAATGGTTTTTAAAA
1 ATATATATTAT-ATAAAT-G-TTTTAAAA
102560 ATTATATATTATATAAATGTTTT
1 A-TATATATTATATAAATGTTTT
102583 CATAACGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
23 8 0.13
24 4 0.07
25 5 0.08
26 3 0.05
27 16 0.27
28 12 0.20
29 12 0.20
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (26 bp):
ATATATATTATATAAATGTTTTAAAA
Found at i:102604 original size:36 final size:36
Alignment explanation
Indices: 102552--102703 Score: 117
Period size: 36 Copynumber: 4.1 Consensus size: 36
102542 TCAAAATGGT
* * * * *
102552 TTTTAAAAATTATATATTATATAAATGTTTTCATAACG
1 TTTTCAAAAGTATATA-T-TATAAATATTTTAAAAACG
*
102590 TTTTCAAAAGTATATATTATATATATTTTAAAAACG
1 TTTTCAAAAGTATATATTATAAATATTTTAAAAACG
* * **
102626 TTTTCAAAAACTATATATTATATAAT-TTTCAAAAATA
1 TTTTC-AAAAGTATATATTATA-AATATTTTAAAAACG
* * * * *
102663 TTTTAAAAACTATATAATATACATATTTTCAAAAATG
1 TTTTCAAAAGTATATATTATAAATATTTT-AAAAACG
102700 TTTT
1 TTTT
102704 AAACTATATA
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
35 2 0.02
36 38 0.40
37 38 0.40
38 16 0.17
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAGTATATATTATAAATATTTTAAAAACG
Found at i:102727 original size:37 final size:36
Alignment explanation
Indices: 102534--102734 Score: 178
Period size: 37 Copynumber: 5.4 Consensus size: 36
102524 TTTTCAAAAA
*
102534 ATATATTTTC-AAAATGGTTTTTAAAAATTATATATTAT
1 ATATATTTTCAAAAAT-G-TTTT-AAAACTATATATTAT
* * * *
102572 ATAAATGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 AT--ATATTTTCAAAAATGTTTT-AAAACTATATATTAT
*
102610 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAATGTTTT--AAAACTATATATTAT
* *
102647 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAATGTTTT-AAAACTATATATTAT
*
102683 ACATATTTTCAAAAATGTTTT-AAACTATATACTATAT
1 ATATATTTTCAAAAATGTTTTAAAACTATATA-T-TAT
*
102720 ATGTATTTTCAAAAA
1 ATATATTTTCAAAAA
102735 CAATTTGCAA
Statistics
Matches: 138, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
35 10 0.07
36 37 0.27
37 58 0.42
38 22 0.16
39 1 0.01
40 10 0.07
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
ATATATTTTCAAAAATGTTTTAAAACTATATATTAT
Found at i:102747 original size:74 final size:71
Alignment explanation
Indices: 102595--102757 Score: 175
Period size: 74 Copynumber: 2.2 Consensus size: 71
102585 TAACGTTTTC
* * *
102595 AAAAGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
1 AAAACTATATAATATACATATTTTAAAAACGTTTT--AAAACTATATATTATATAATTTTCAAAA
* *
102660 ATATTTTA
64 ACAATTTA
* *
102668 AAAACTATATAATATACATATTTTCAAAAATGTTTT-AAACTATATACTATATATGTATTTTCAA
1 AAAACTATATAATATACATATTTT-AAAAACGTTTTAAAACTATATA-T-TATAT-AATTTTCAA
*
102732 AAACAATTTG
62 AAACAATTTA
* *
102742 CAAACTGTATAATATA
1 AAAACTATATAATATA
102758 TATGTGCATA
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
71 10 0.13
72 1 0.01
73 26 0.34
74 39 0.51
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (71 bp):
AAAACTATATAATATACATATTTTAAAAACGTTTTAAAACTATATATTATATAATTTTCAAAAAC
AATTTA
Found at i:102757 original size:37 final size:34
Alignment explanation
Indices: 102632--102758 Score: 101
Period size: 37 Copynumber: 3.5 Consensus size: 34
102622 AACGTTTTCA
* * *
102632 AAAACTATATATTATATAATTTTCAAAAATATTTT
1 AAAACTATATAATATATTATTTTCAAAAA-AATTT
* **
102667 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATA-TTATTTTCAAAAAAATTT
*
102703 TAAACTATATACTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATAT-TATTTTCAAAAA-AATTT
* *
102741 GCAAACTGTATAATATAT
1 -AAAACTATATAATATAT
102759 ATGTGCATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
35 10 0.14
36 18 0.24
37 34 0.46
38 3 0.04
39 9 0.12
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (34 bp):
AAAACTATATAATATATTATTTTCAAAAAAATTT
Found at i:103554 original size:248 final size:250
Alignment explanation
Indices: 103146--104073 Score: 1239
Period size: 248 Copynumber: 3.7 Consensus size: 250
103136 CAAATAGCTT
* * **
103146 TTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT
1 TTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT
* * * *
103211 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTT-GGAGCTGAGCGT
66 CTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTCGAAGCTGAACGT
103275 AGTCGAACTCAAAGGTCTTTGGT-AGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
131 AGTCGAACTCAAAGGTCTTTGGTGA-CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
103339 ATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCC
195 ATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCC
103395 TTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT
1 TTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT
* * * *
103460 C-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTT-GGAGCTGAGCGT
66 CTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTCGAAGCTGAACGT
103523 AGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATA
131 AGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATA
103588 TGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCC
196 TGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCC
*
103643 TTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTAAACGTAGTCGAACTCGAGGGT
1 TTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT
* *
103708 CTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGA
66 C--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTCGAAGCTGA
* * * * * * * * *
103773 ACGTAGTCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAAT
127 ACGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
* * * * * * * *
103835 GATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GGTGACAGATAACCC
192 GATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCC
* * * * * * ** * **
103892 TTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTT-GAAGCTGAGTGTAATCGAACTTAAGGG
1 TTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGAGGG
* *
103956 TCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTG
65 TC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTCGAAGCTG
* * * *
104021 AACGTAGTCGAACTCGAAGGTC-TTGGTGGGCAGATAGCCCTTCTGGCCTTGAG
126 AACGTAGTCGAACTCAAAGGTCTTTGGT-GACAGATAACCCTTCTAGCCTTGAG
104074 CTAAGCTGCA
Statistics
Matches: 623, Mismatches: 44, Indels: 21
0.91 0.06 0.03
Matches are distributed among these distances:
248 247 0.40
249 210 0.34
250 35 0.06
251 35 0.06
252 21 0.03
253 47 0.08
254 28 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (250 bp):
TTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT
CTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTCGAAGCTGAACGT
AGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATA
TGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCC
Found at i:103916 original size:334 final size:333
Alignment explanation
Indices: 103146--104064 Score: 1431
Period size: 334 Copynumber: 2.8 Consensus size: 333
103136 CAAATAGCTT
* * * *
103146 TTCTCGACTTAAGCTATGT-TGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGG
1 TTCTCGACTTAAGCTAT-TCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCAAAGG
* * * * * * * * *
103210 TCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGA
64 TCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGA
* * * * * * * * * * *
103271 GCGTAGTCGAACTCAAAGGTCTTT-GGTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
129 GTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAA
* ** * **
103335 TGATATGCCCTT-GAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCT
194 TGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTAGTTGGCAGATAACCCTTCT
103399 TGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTG
258 TGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTG
103464 GCAGATAGCCC
323 GCAGATAGCCC
103475 TTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
1 TTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
103540 TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGT
66 TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGT
103605 GTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
131 GTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
*
103670 ATGTGCCTTCGAAGCTAAACGTAGTCGAACTCGAGGGTCTTTAGTTGGCAGATAACCCTTCTTGA
196 ATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTAGTTGGCAGATAACCCTTCTTGA
103735 CTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGC
261 CTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTC-TTGGC
103800 AGATAGCCC
325 AGATAGCCC
103809 TTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
1 TTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
103874 TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGT
66 TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGT
103939 GTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
131 GTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
* * * *
104004 ATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAAGGTC-TTGGTGGGCAGATAGCCCTTCT
196 ATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTAGTTGGCAGATAACCCTTCT
104065 GGCCTTGAGC
Statistics
Matches: 546, Mismatches: 36, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
328 29 0.05
329 35 0.06
330 1 0.00
331 34 0.06
332 35 0.06
333 166 0.30
334 246 0.45
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (333 bp):
TTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGT
GTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
ATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTAGTTGGCAGATAACCCTTCTTGA
CTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTGGCA
GATAGCCC
Found at i:110536 original size:26 final size:27
Alignment explanation
Indices: 110490--110540 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
110480 AATAATAATA
110490 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
110518 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
110541 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:110677 original size:35 final size:38
Alignment explanation
Indices: 110555--110885 Score: 113
Period size: 37 Copynumber: 8.8 Consensus size: 38
110545 TTTTTTAAAA
110555 AAAACTATATATTATATAT-ATTTTC-AAAATGGTTTT-
1 AAAACTATATATTATATATAATTTTCAAAAAT-GTTTTC
* *
110591 -----TATATATTATATA-AATGTTTTC-ATAACGTTTTC
1 AAAACTATATATTATATATAA--TTTTCAAAAATGTTTTC
*
110624 AAAAGTATATATTATATAT-ATTTT-AAAAATGTTTTC
1 AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
*
110660 AAAAACTATATA-T-TATATAATTTTCAAAAAATATATTTTC
1 -AAAACTATATATTATATATAATTTTC--AAAA-ATGTTTTC
* * * * *
110700 AAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTC-ATAACGTTTTC
1 AAAA------CT--ATA-TAT-TA-TATAT-AATTTT--CAAAAATGTTTTC
* *
110751 AAAA--GTATATTATATAT-ATTTT--AAAACGTTTTC
1 AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
* *
110784 AAAA--ACTATA-TAT-TATAATTTTCAAAAATATTTTA
1 AAAACTA-TATATTATATATAATTTTCAAAAATGTTTTC
* *
110819 AAAACTATATAATATACAT-ATTTTCAAAAATGTTTT-
1 AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
* *
110855 -AAACTATATACTATATATGTATTTTCAAAAA
1 AAAACTATATATTATATAT-AATTTTCAAAAA
110886 CAATTTGCAA
Statistics
Matches: 228, Mismatches: 24, Indels: 85
0.68 0.07 0.25
Matches are distributed among these distances:
31 14 0.06
32 8 0.04
33 30 0.13
34 4 0.02
35 33 0.14
36 27 0.12
37 41 0.18
38 21 0.09
39 10 0.04
40 10 0.04
41 1 0.00
45 1 0.00
47 2 0.01
48 2 0.01
50 1 0.00
51 10 0.04
52 7 0.03
53 5 0.02
55 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAACTATATATTATATATAATTTTCAAAAATGTTTTC
Found at i:110687 original size:25 final size:25
Alignment explanation
Indices: 110655--110731 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
110645 TTTAAAAATG
*
110655 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
110680 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
110707 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
110732 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:110699 original size:15 final size:16
Alignment explanation
Indices: 110674--110703 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
110664 ACTATATATT
110674 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
110690 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
110704 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:110738 original size:27 final size:26
Alignment explanation
Indices: 110637--110738 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
110627 AGTATATATT
* *
110637 ATATATATTTTAAAAATGTTTTCAAAA
1 ATATATATTATATAAATGTTTT-AAAA
*
110664 ACTATATATTATAT-AAT-TTTCAAAA
1 A-TATATATTATATAAATGTTTTAAAA
*
110689 A-ATATATTTTCA-AAATGGTTTTTAAAA
1 ATATATATTAT-ATAAAT-G-TTTTAAAA
110716 ATTATATATTATATAAATGTTTT
1 A-TATATATTATATAAATGTTTT
110739 CATAACGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
23 8 0.13
24 4 0.07
25 5 0.08
26 3 0.05
27 16 0.27
28 12 0.20
29 12 0.20
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (26 bp):
ATATATATTATATAAATGTTTTAAAA
Found at i:110805 original size:33 final size:35
Alignment explanation
Indices: 110690--110872 Score: 130
Period size: 34 Copynumber: 5.2 Consensus size: 35
110680 TTTTCAAAAA
* * *
110690 ATATATTTTCAAAATGGTTTTTAAAAATTATATATT
1 ATATATTTTCAAAA-CGTTTTCAAAAACTATATATT
* *
110726 ATATAAATGTTTTCATAACGTTTTC-AAAAGTATAT-TAT
1 ATAT--A--TTTTCAAAACGTTTTCAAAAACTATATAT-T
110764 ATATATTTT-AAAACGTTTTCAAAAACTATATATT
1 ATATATTTTCAAAACGTTTTCAAAAACTATATATT
* *
110798 ATA-ATTTTCAAAA-ATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAACGT-TTTCAAAAACTATAT-AT-T
* * *
110834 ACATATTTTCAAAAATGTTTT---AAACTATATACT
1 ATATATTTTC-AAAACGTTTTCAAAAACTATATATT
110867 ATATAT
1 ATATAT
110873 GTATTTTCAA
Statistics
Matches: 121, Mismatches: 12, Indels: 31
0.74 0.07 0.19
Matches are distributed among these distances:
33 22 0.18
34 36 0.30
35 12 0.10
36 8 0.07
37 7 0.06
38 22 0.18
39 6 0.05
40 8 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
ATATATTTTCAAAACGTTTTCAAAAACTATATATT
Found at i:110878 original size:37 final size:36
Alignment explanation
Indices: 110785--110908 Score: 112
Period size: 37 Copynumber: 3.4 Consensus size: 36
110775 AACGTTTTCA
*
110785 AAAACTATAT-AT-TATA-ATTTTCAAAAATATTTT
1 AAAACTATATAATATACATATTTTCAAAAATATTTT
*
110818 AAAAACTATATAATATACATATTTTCAAAAATGTTTT
1 -AAAACTATATAATATACATATTTTCAAAAATATTTT
** * *
110855 -AAACTATATACTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATA--ATATACATATTTTCAAAAA-TATTTT
* *
110893 CAAACTGTATAATATA
1 AAAACTATATAATATA
110909 TATGTGCATA
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
34 10 0.13
35 12 0.16
36 3 0.04
37 38 0.51
38 3 0.04
39 9 0.12
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (36 bp):
AAAACTATATAATATACATATTTTCAAAAATATTTT
Done.