Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012185.1 Kokia drynarioides strain JFW-HI SEQ_127186, 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: 264553
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:871 original size:129 final size:130
Alignment explanation
Indices: 624--873 Score: 373
Period size: 129 Copynumber: 1.9 Consensus size: 130
614 CTGTTTTATA
*
624 ACTCTAGTGTCGGGGGAAATGAGGTGAGAATGAATTCCCAATACACTGAAGCCATTCACTGAACA
1 ACTCTAGTGTCGGGAGAAATGAGGTGAGAATGAATTCCCAATACACTGAAGCCATTCACTGAACA
* *
689 GGCACTTAGACTGTTGTTTTCAATTTTAATTTAACTGTTTATATTTTACTTGAATTTGTTGCATG
66 GGCACTTAGACTCTTGTTTTCAATTTTAATTTAACTGTTTATATTTGACTTGAATTTGTTGCATG
* * *
754 ACTCTAGTGTTGGGAG-AATGAGGTGAGAATGAATTCCCTAA-CCACTGAAGCCATTCATTGAAC
1 ACTCTAGTGTCGGGAGAAATGAGGTGAGAATGAATTCCC-AATACACTGAAGCCATTCACTGAAC
* *
817 AGGCACTTAAGATTCTTGTTTT-TATTTTAATTTAA-TGGTTTATATTTGACTTGAATT
65 AGGCACTT-AGACTCTTGTTTTCAATTTTAATTTAACT-GTTTATATTTGACTTGAATT
874 GAGGACTCCT
Statistics
Matches: 109, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
128 1 0.01
129 81 0.74
130 27 0.25
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (130 bp):
ACTCTAGTGTCGGGAGAAATGAGGTGAGAATGAATTCCCAATACACTGAAGCCATTCACTGAACA
GGCACTTAGACTCTTGTTTTCAATTTTAATTTAACTGTTTATATTTGACTTGAATTTGTTGCATG
Found at i:2453 original size:45 final size:45
Alignment explanation
Indices: 2399--2496 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
2389 ACCACTATGT
* **
2399 TCTCTGTTTTGCAAACATCTATGTATTTTTTTTTTCTTATTATCA
1 TCTCAGTTTTGCAAACATCTATGTATTTTCCTTTTCTTATTATCA
* *
2444 TCTCAGTTTTGCAAACATCTATGTGTTTTCCTTTTCTTATTATCT
1 TCTCAGTTTTGCAAACATCTATGTATTTTCCTTTTCTTATTATCA
2489 TCT-AGTTT
1 TCTCAGTTT
2497 AGCAGATACC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 5 0.10
45 43 0.90
ACGTcount: A:0.18, C:0.17, G:0.08, T:0.56
Consensus pattern (45 bp):
TCTCAGTTTTGCAAACATCTATGTATTTTCCTTTTCTTATTATCA
Found at i:12990 original size:21 final size:21
Alignment explanation
Indices: 12964--13011 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
12954 CCTTTAAGCT
*
12964 CAAACCAAAGTGAACCAAGTC
1 CAAACCAAAGCGAACCAAGTC
* *
12985 CAAACCCATGCGAACCAAGTC
1 CAAACCAAAGCGAACCAAGTC
13006 CAAACC
1 CAAACC
13012 CAACCTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.35, G:0.12, T:0.08
Consensus pattern (21 bp):
CAAACCAAAGCGAACCAAGTC
Found at i:13570 original size:14 final size:14
Alignment explanation
Indices: 13551--13580 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13541 TGCTGTTTGA
13551 GATATGTTGATATT
1 GATATGTTGATATT
13565 GATATGTTGATATT
1 GATATGTTGATATT
13579 GA
1 GA
13581 GACGATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
GATATGTTGATATT
Found at i:17856 original size:21 final size:21
Alignment explanation
Indices: 17818--17858 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17808 GACCTTTACT
*
17818 GATACAAGTGATAGTTCTACG
1 GATACAAGTGATACTTCTACG
17839 GATACAAGTGACT-CTTCTAC
1 GATACAAGTGA-TACTTCTAC
17859 CGAAATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
GATACAAGTGATACTTCTACG
Found at i:18627 original size:53 final size:53
Alignment explanation
Indices: 18508--18913 Score: 544
Period size: 53 Copynumber: 7.7 Consensus size: 53
18498 CAGACTTGAG
* ** * * **
18508 AACTCACGATGACACAGAGTCATCAAACCTTTAATCCATGAT-GGATTTGTAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
* * * * * *
18560 ATCTCACGATGACACAAAGTCATCGAACCCTTAATACGTAATAGGATTCGTAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
* * *
18613 AACTCAAGATGACACATAGTCATCGGGCCTTTAATCCATAATAGGATTCATAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
* *
18666 AACTCACGATGACATATAGTCATCGGACCCTTAATCCGTAATAGGATTCATAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
* * *
18719 AACTCACGATGACACATAGTCATTGGACCCTTAATTCGTAATAGGATTCATAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
* * *
18772 AAATCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCATAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
* ** *
18825 AACTCACAATGACACATAGTCATCAAACCTTTAATCCGTAACAGGATTCATAT
1 AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
*
18878 AACTCACGATGACACATAGTTATCGGACCTTTAATC
1 AACTCACGATGACACATAGTCATCGGACCTTTAATC
18914 TTTGGCAAGG
Statistics
Matches: 311, Mismatches: 42, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
52 35 0.11
53 276 0.89
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (53 bp):
AACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCATAT
Found at i:25955 original size:106 final size:107
Alignment explanation
Indices: 25817--26131 Score: 368
Period size: 106 Copynumber: 3.0 Consensus size: 107
25807 TTCACATTTG
* * *
25817 ATAACTCACAATGACA-TTGAGTCATCGGACCTTTATTCCATGAT-GGATTCGTATATCTCACGA
1 ATAACTCACAATGACACAT-AGTCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGA
* *
25880 TAACACAAAGTCATCGGACCCTTTAATCCATAATAGGATTCAT
65 TGACACATAGTCATCGGACCCTTTAATCCATAATAGGATTCAT
* * * *
25923 ATAACTCACGATGACACATAGTCATCGAACCTTTAATCCATGATAGAATTTGTATAACTCACGAT
1 ATAACTCACAATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGAT
* * *
25988 GACACATAGTCATCGGA-CCTTTAATCTATGATAAGATTCAT
66 GACACATAGTCATCGGACCCTTTAATCCATAATAGGATTCAT
* ** * * * * * * *
26029 ATAGCTCGTAACGACACATAATCATCGGACCCTTAATCCGTAATAGGATTCATATAACTCATGAT
1 ATAACTCACAATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGAT
** *
26094 GACACATAGTCATTAGACCC-TTAATCCGTAATAGGATT
66 GACACATAGTCATCGGACCCTTTAATCCATAATAGGATT
26132 TGTAACACCC
Statistics
Matches: 174, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
106 139 0.80
107 35 0.20
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (107 bp):
ATAACTCACAATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGAT
GACACATAGTCATCGGACCCTTTAATCCATAATAGGATTCAT
Found at i:25956 original size:53 final size:53
Alignment explanation
Indices: 25817--26131 Score: 303
Period size: 53 Copynumber: 5.9 Consensus size: 53
25807 TTCACATTTG
* * * * * *
25817 ATAACTCACAATGACA-TTGAGTCATCGGACCTTTATTCCATGAT-GGATTCGT
1 ATAACTCACGATGACACAT-AGTCATCGAACCTTTAATCCATAATAGGATTCAT
* * * *
25869 ATATCTCACGATAACACAAAGTCATCGGACCCTTTAATCCATAATAGGATTCAT
1 ATAACTCACGATGACACATAGTCATC-GAACCTTTAATCCATAATAGGATTCAT
* * **
25923 ATAACTCACGATGACACATAGTCATCGAACCTTTAATCCATGATAGAATTTGT
1 ATAACTCACGATGACACATAGTCATCGAACCTTTAATCCATAATAGGATTCAT
* * * *
25976 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCTATGATAAGATTCAT
1 ATAACTCACGATGACACATAGTCATCGAACCTTTAATCCATAATAGGATTCAT
* *** * * * * *
26029 ATAGCTCGTAACGACACATAATCATCGGACCCTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACATAGTCATCGAACCTTTAATCCATAATAGGATTCAT
* * * *
26082 ATAACTCATGATGACACATAGTCAT-TAGACCCTTAATCCGTAATAGGATT
1 ATAACTCACGATGACACATAGTCATCGA-ACCTTTAATCCATAATAGGATT
26132 TGTAACACCC
Statistics
Matches: 217, Mismatches: 42, Indels: 7
0.82 0.16 0.03
Matches are distributed among these distances:
52 20 0.09
53 167 0.77
54 30 0.14
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (53 bp):
ATAACTCACGATGACACATAGTCATCGAACCTTTAATCCATAATAGGATTCAT
Found at i:26106 original size:159 final size:157
Alignment explanation
Indices: 25812--26106 Score: 409
Period size: 159 Copynumber: 1.9 Consensus size: 157
25802 TTCCATTCAC
* * * * *
25812 ATTTGATAACTCACAATGACATTGAGTCATCGGACCTTTATTCCATGATGGATTCGTATATCTCA
1 ATTTGATAACTCACAATGACAATGAGTCATCGGACCTTTAATCCATGATAGATTCATATAGCT-A
*
25877 CGATAACACAAAGTCATCGGACCCTTTAATCCATAATAGGATTCATATAACTCACGATGACACAT
65 CGATAACACAAAATCATCGGACCCTTTAATCCATAATAGGATTCATATAACTCACGATGACACAT
25942 AGTCATCGAACCTTTAATCCATGATAGA
130 AGTCATCGAACCTTTAATCCATGATAGA
* *
25970 ATTTGTATAACTCACGATGACACAT-AGTCATCGGACCTTTAATCTATGATAAGATTCATATAGC
1 ATTTG-ATAACTCACAATGACA-ATGAGTCATCGGACCTTTAATCCATGAT-AGATTCATATAGC
* *
26034 T-CG-TAACGACACATAATCATCGGACCC-TTAATCCGTAATAGGATTCATATAACTCATGATGA
63 TACGATAAC-ACA-A-AATCATCGGACCCTTTAATCCATAATAGGATTCATATAACTCACGATGA
26096 CACATAGTCAT
125 CACATAGTCAT
26107 TAGACCCTTA
Statistics
Matches: 121, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
157 4 0.03
158 10 0.08
159 83 0.69
160 24 0.20
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (157 bp):
ATTTGATAACTCACAATGACAATGAGTCATCGGACCTTTAATCCATGATAGATTCATATAGCTAC
GATAACACAAAATCATCGGACCCTTTAATCCATAATAGGATTCATATAACTCACGATGACACATA
GTCATCGAACCTTTAATCCATGATAGA
Found at i:30358 original size:46 final size:46
Alignment explanation
Indices: 30291--30404 Score: 174
Period size: 46 Copynumber: 2.5 Consensus size: 46
30281 GCTTCTCTGA
* * * *
30291 GATTGTAGCTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTG
1 GATTGTGGCTTCAATCTGCCCCTCTTGACTTAGAGGAAAAAGATTG
*
30337 GATTGTGGCTTCAATTTGCCCCTCTTGACTTAGAGGAAAAAGATTG
1 GATTGTGGCTTCAATCTGCCCCTCTTGACTTAGAGGAAAAAGATTG
*
30383 GATGGTGGCTTCAATCTGCCCC
1 GATTGTGGCTTCAATCTGCCCC
30405 ATGATCGGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (46 bp):
GATTGTGGCTTCAATCTGCCCCTCTTGACTTAGAGGAAAAAGATTG
Found at i:30586 original size:78 final size:78
Alignment explanation
Indices: 30377--31054 Score: 541
Period size: 78 Copynumber: 8.6 Consensus size: 78
30367 TAGAGGAAAA
* ** * *
30377 AGATTGGATGGTGGCTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGAATGATGTCTTTAATC
1 AGATTGG-T-GTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTG---GATG-CTTCAATC
* *
30441 TGCCCCATAATCAGGGTAAG
59 TGCCCCATGATCGGGGTAAG
* * * * ** *
30461 AGATTAG-AT-ACTTCAATCTTCCC-CATGATCGGGGTAAGAGATTGGATGCTTCAATCTGCCCC
1 AGATTGGTGTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCC
30523 ATGATCGGGGTAAG
65 ATGATCGGGGTAAG
* * * * *
30537 AGATTGGTGTGTATTCAATCTGCCTTCTGGTTAGGGTAACAGATTGGATGCTTCAATTTGCCCCA
1 AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCA
* *
30602 TGATCAGGGTATG
66 TGATCGGGGTAAG
* * * * *
30615 AGATTGGTGTGTCTTTAATCTACCCTCTGATTAGGATAAAAGATTAGATGCTTCAATCTGCTCCA
1 AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCA
* *
30680 TGATCGAGATATA-
66 TGATCGGGGTA-AG
* * * * * *
30693 AGATTGGTGTGTCTTCAGTTTGCCTTTTGATTAGGGTAAAAGATTGGATGCTTTAATCTGCCTCA
1 AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCA
**
30758 TGAGT-GACGTAAG
66 TGA-TCGGGGTAAG
* * ** * * *
30771 AGATTGGATAATGGCTTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGACTTCAGTCTAC
1 AGATTGG-T-GTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGGATG-CTTCAATCTGC
* ** *
30835 CTCACAATCGAGGTAAG
62 CCCATGATCGGGGTAAG
** * * *
30852 AGATTTAATGATGTTTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATGCCTT-AATCTACC
1 AGA-TTGGTG-TGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATG-CTTCAATCTGCC
* *
30916 CCATGATAGGGGTATG
63 CCATGATCGGGGTAAG
* * * *
30932 AGATTGGTGTGTCTTTAATCTGCCCTCTAATTAGGGTAAAAGATTGGTGTGTCTTCAATCTACCC
1 AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGG-ATG-CTTCAATCTGCCC
** *
30997 TC-TGATTAGGGTAAA
64 -CATGATCGGGGTAAG
*
31012 AGATTGG-ATG-CTTCAATCTGCCCTCTGATTAGGGTAAAAGATT
1 AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATT
31055 AATGTGTCTT
Statistics
Matches: 483, Mismatches: 94, Indels: 40
0.78 0.15 0.06
Matches are distributed among these distances:
76 31 0.06
77 6 0.01
78 250 0.52
79 14 0.03
80 111 0.23
81 62 0.13
82 3 0.01
84 6 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (78 bp):
AGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCA
TGATCGGGGTAAG
Found at i:30950 original size:40 final size:40
Alignment explanation
Indices: 30299--31406 Score: 574
Period size: 38 Copynumber: 27.9 Consensus size: 40
30289 GAGATTGTAG
* *
30299 CTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTGGATTGTGG
1 CTTCAATCTG-CCC-CATGA-TTA-GGGTAAAAGATTGG--TGTGT
* * * *
30345 CTTCAATTTGCCCCTCTTGACTTAGAGGAAAAAGATTGGATGGTGG
1 CTTCAATCTG-CCC-CATGA-TTAG-GGTAAAAGATTGG-T-GTGT
** * *
30391 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGAATGATGT
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTG-GTG-TGT
* * * * * * *
30433 CTTTAATCTGCCCCATAATCAGGGTAAGAGATTAG-AT-A
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
* ** * *
30471 CTTCAATCTTCCCCATGATCGGGGTAAGAGATTGG-ATG-
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
** *
30509 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
* * * * *
30549 ATTCAATCTGCCTTC-TGGTTAGGGTAACAGATTGG-ATG-
1 CTTCAATCTGCC-CCATGATTAGGGTAAAAGATTGGTGTGT
* * **
30587 CTTCAATTTGCCCCATGATCAGGGTATGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
* * * * *
30627 CTTTAATCTACCCTC-TGATTAGGATAAAAGATTAG-ATG-
1 CTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGTGTGT
* * * *
30665 CTTCAATCTGCTCCATGA-TCGAGATATAAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATTAG-GGTAAAAGATTGGTGTGT
* * *** *
30705 CTTCAGTTTGCCTTTTGATTAGGGTAAAAGATTGG-ATG-
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
* * * * * * *
30743 CTTTAATCTGCCTCATGAGT-GACGTAAGAGATTGGATAATGG
1 CTTCAATCTGCCCCATGATTAG-GGTAAAAGATTGG-T-GTGT
** * * *
30785 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATGA
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
* * * * * * * **
30824 CTTCAGTCTACCTCA-CAATCGAGGTAAGAGATTTAATGATGT
1 CTTCAATCTGCCCCATGATTAG-GGTAAAAGA-TTGGTG-TGT
* * * *
30866 TTTCAATTTGCCCTC-TGATTAGGGTAAAAGATTGG-ATGC
1 CTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGTGTGT
* **
30905 CTT-AATCTACCCCATGA-TAGGGGTATGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATTA-GGGTAAAAGATTGGTGTGT
* *
30944 CTTTAATCTGCCCTC-TAATTAGGGTAAAAGATTGGTGTGT
1 CTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGTGTGT
* *
30984 CTTCAATCTACCCTC-TGATTAGGGTAAAAGATTGG-ATG-
1 CTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGTGTGT
**
31022 CTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTAATGTGT
1 CTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGGTGTGT
* ** *
31062 CTTCAGTCTGCCCTTTGATTAGGGTAAAAGATTGG-ATG-
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
** ** **
31100 CTTCAATCTGCCCCATGATCGGGGTATGAGATTGACGTGT
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
* * *
31140 C-T---T-TGCCTTC-TAATTAGGGTAAAAGATTGG-AT-T
1 CTTCAATCTGCC-CCATGATTAGGGTAAAAGATTGGTGTGT
* *
31173 CTTCAATCTGCCCCAT-AGTCAGGGTATAAGATTGGTGTGT
1 CTTCAATCTGCCCCATGA-TTAGGGTAAAAGATTGGTGTGT
* * *
31213 CTTCAATCTG-CCCTTTACTTAGGGTAAAAGATTGG-ATG-
1 CTTCAATCTGCCCCATGA-TTAGGGTAAAAGATTGGTGTGT
* * *
31251 CTTCAATCTACCCCATAATCT-GGGTAAGAGATTGGATGATGT
1 CTTCAATCTGCCCCATGAT-TAGGGTAAAAGATTGG-TG-TGT
* * * *
31293 CTTCAATCTACCCCATGATCAGGGTAAGAGATTGGAT-AG-
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGG-TGTGT
* * **
31332 CTTCAATCTGCCCTATGATTGGGGTATGAGATTGGTGTGT
1 CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
*
31372 CTTCAATCTACCCTC-TGATTAGGGTAAAAGATTGG
1 CTTCAATCTGCCC-CATGATTAGGGTAAAAGATTGG
31407 ATACTTCTAT
Statistics
Matches: 827, Mismatches: 174, Indels: 128
0.73 0.15 0.11
Matches are distributed among these distances:
33 2 0.00
34 2 0.00
35 18 0.02
36 2 0.00
37 11 0.01
38 268 0.32
39 99 0.12
40 224 0.27
41 15 0.02
42 123 0.15
43 7 0.01
44 4 0.00
45 5 0.01
46 47 0.06
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (40 bp):
CTTCAATCTGCCCCATGATTAGGGTAAAAGATTGGTGTGT
Found at i:31061 original size:78 final size:78
Alignment explanation
Indices: 30867--31422 Score: 507
Period size: 78 Copynumber: 7.2 Consensus size: 78
30857 TAATGATGTT
* *
30867 TTCAATTTGCCCTCTGATTAGGGTAAAAGATTG--GATGCCTT-AATCTACCC-CATGA-TAGGG
1 TTCAATCTGCCCTCTGATTAGGGTAAAAGATTGATG-TGTCTTCAATCTACCCTC-TGATTA-GG
** *
30927 GTATGAGATTGGTGTGTC
63 GTAAAAGATTGG-ATG-C
* * *
30945 TTTAATCTGCCCTCTAATTAGGGTAAAAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTA
1 TTCAATCTGCCCTCTGATTAGGGTAAAAGATTGATGTGTCTTCAATCTACCCTCTGATTAGGGTA
31010 AAAGATTGGATGC
66 AAAGATTGGATGC
* * * *
31023 TTCAATCTGCCCTCTGATTAGGGTAAAAGATTAATGTGTCTTCAGTCTGCCCTTTGATTAGGGTA
1 TTCAATCTGCCCTCTGATTAGGGTAAAAGATTGATGTGTCTTCAATCTACCCTCTGATTAGGGTA
31088 AAAGATTGGATGC
66 AAAGATTGGATGC
** ** * * * *
31101 TTCAATCTGCCC-CATGATCGGGGTATGAGATTGACGTGTC-T---T-TGCCTTCTAATTAGGGT
1 TTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGATGTGTCTTCAATCTACCCTCTGATTAGGGT
*
31160 AAAAGATTGGATTC
65 AAAAGATTGGATGC
* * * * *
31174 TTCAATCTGCCC-CAT-AGTCAGGGTATAAGATTGGTGTGTCTTCAATCTGCCCT-TTACTTAGG
1 TTCAATCTGCCCTC-TGA-TTAGGGTAAAAGATTGATGTGTCTTCAATCTACCCTCTGA-TTAGG
31236 GTAAAAGATTGGATGC
63 GTAAAAGATTGGATGC
* * * *
31252 TTCAATCTACCC-CATAATCT-GGGTAAGAGATTGGATGATGTCTTCAATCTACCC-CATGATCA
1 TTCAATCTGCCCTC-TGAT-TAGGGTAAAAGATT-GATG-TGTCTTCAATCTACCCTC-TGATTA
*
31314 GGGTAAGAGATTGGATAGC
61 GGGTAAAAGATTGGAT-GC
* * ** *
31333 TTCAATCTGCCCTATGATTGGGGTATGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTA
1 TTCAATCTGCCCTCTGATTAGGGTAAAAGATTGATGTGTCTTCAATCTACCCTCTGATTAGGGTA
*
31398 AAAGATTGGATAC
66 AAAGATTGGATGC
* *
31411 TTCTATTTGCCC
1 TTCAATCTGCCC
31423 CATGATCGGG
Statistics
Matches: 405, Mismatches: 50, Indels: 46
0.81 0.10 0.09
Matches are distributed among these distances:
72 1 0.00
73 61 0.15
74 2 0.00
77 5 0.01
78 195 0.48
79 47 0.12
80 62 0.15
81 32 0.08
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (78 bp):
TTCAATCTGCCCTCTGATTAGGGTAAAAGATTGATGTGTCTTCAATCTACCCTCTGATTAGGGTA
AAAGATTGGATGC
Found at i:31227 original size:151 final size:151
Alignment explanation
Indices: 31001--31443 Score: 536
Period size: 151 Copynumber: 2.9 Consensus size: 151
30991 CTACCCTCTG
* **
31001 ATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTAATGTGTCTT
1 ATTAGGGTAAAAGATTGGATGCTTCAATCTGCCC-CATGATTAGGGTATAAGATTGGTGTGTCTT
*
31065 CAGTCTGCCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTATGAG
65 CAATCTGCCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTATGAG
**
31130 ATTGACG-TGTCTTTGCCTTCTA-
130 ATTGACGATGTC-TT-CAATCTAC
* *
31152 ATTAGGGTAAAAGATTGGATTCTTCAATCTGCCCCAT-AGTCAGGGTATAAGATTGGTGTGTCTT
1 ATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGA-TTAGGGTATAAGATTGGTGTGTCTT
* * * *
31216 CAATCTGCCCTTT-ACTTAGGGTAAAAGATTGGATGCTTCAATCTACCCCATAATCTGGGTAAGA
65 CAATCTGCCCTTTGA-TTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTATGA
*
31280 GATTGGATGATGTCTTCAATCTACCCC
129 GATT-GACGATGTCTTCAATCTA---C
* * * *
31307 ATGATCAGGGTAAGAGATTGGATAGCTTCAATCTGCCCTATGATTGGGGTATGAGATTGGTGTGT
1 AT--T-AGGGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATTAGGGTATAAGATTGGTGTGT
* * * * *
31372 CTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGATACTTCTATTTGCCCCATGATCGGGGTAT
62 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAT
31437 GAGATTG
127 GAGATTG
31444 GATGGTAGCT
Statistics
Matches: 249, Mismatches: 28, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
150 3 0.01
151 121 0.49
152 5 0.02
153 4 0.02
155 2 0.01
157 1 0.00
158 17 0.07
159 94 0.38
160 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (151 bp):
ATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTAGGGTATAAGATTGGTGTGTCTTC
AATCTGCCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTATGAGA
TTGACGATGTCTTCAATCTAC
Found at i:31675 original size:42 final size:41
Alignment explanation
Indices: 31586--31700 Score: 108
Period size: 42 Copynumber: 2.8 Consensus size: 41
31576 CAGGGACGTA
* * * *
31586 AGATTCGTCTTTTCAGCTTCAATCTAGCCTTTTACAGCTTTG
1 AGATTCGCCTTTACAGCTTCAATAT-GCTTTTTACAGCTTTG
* *
31628 TGATTCGCCTTTACAGCTTCAATATGCTTTTATACA-ATCTTG
1 AGATTCGCCTTTACAGCTTCAATATGCTTTT-TACAGCT-TTG
* *
31670 AGATTCACCTTTAC-GACTTCAATTTGCTTTT
1 AGATTCGCCTTTACAG-CTTCAATATGCTTTT
31701 CCTTATCTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 7 0.11
42 54 0.89
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (41 bp):
AGATTCGCCTTTACAGCTTCAATATGCTTTTTACAGCTTTG
Found at i:31795 original size:49 final size:49
Alignment explanation
Indices: 31754--32107 Score: 272
Period size: 49 Copynumber: 7.2 Consensus size: 49
31744 TTCCTTTCAC
* * *
31754 ATCTCTAGGGTATAAGGTTTGCCGTTACGGCTTCAACCTTTCCC-TCTAT
1 ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCATC-AT
* * * * * *
31803 ATCT-TCATGGTACAAGATTCGTCTTTACGGCTTTAATCTTTCCCATCACT
1 ATCTCT-AAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCATCA-T
* * *
31853 -TCTCTAATGTACAAGGTTCGTCGTTGCGGCTTCAACCTTTCCC-TCCAT
1 ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCAT-CAT
* * * * *** * *
31901 GTCTCTATGGTACAAGATTCGCTGTTACAAATTCAATC-TTCCCATCAC
1 ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCATCAT
* ** *
31949 GTCTCTAAGGTACAAGGTTCGTTGTTACGGCTTTAACCTTTCCC-TCCAT
1 ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCAT-CAT
* * * * ** *
31998 ATCTCCACGGTACAAGATTCGCCATTACAACTTCAATCTTTCCCATCAT
1 ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCATCAT
* * * *
32047 GTCCCTAAGGTACAAGGTTTGCCGTTACGACTTCAACCTTTCCC-TCTAT
1 ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCATC-AT
*
32096 ATCTCTAGGGTA
1 ATCTCTAAGGTA
32108 TTATATTTGC
Statistics
Matches: 236, Mismatches: 58, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
48 43 0.18
49 188 0.80
50 5 0.02
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (49 bp):
ATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCATCAT
Found at i:32100 original size:98 final size:98
Alignment explanation
Indices: 31755--32100 Score: 426
Period size: 98 Copynumber: 3.5 Consensus size: 98
31745 TCCTTTCACA
* * * * *
31755 TCTCTAGGGTATAAGGTTTGCCGTTACGGCTTCAACCTTTCCCTCTATATCTTCATGGTACAAGA
1 TCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGA
* * ** *
31820 TTCGTCTTTACGGCTTTAATCTTTCCCATCACT-
66 TTCGCCATTACAACTTCAATCTTTCCCATCA-TG
* * * * *
31853 TCTCTAATGTACAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCATGTCTCTATGGTACAAGA
1 TCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGA
** * *
31918 TTCGCTGTTACAAATTCAATC-TTCCCATCACG
66 TTCGCCATTACAACTTCAATCTTTCCCATCATG
** * *
31950 TCTCTAAGGTACAAGGTTCGTTGTTACGGCTTTAACCTTTCCCTCCATATCTCCACGGTACAAGA
1 TCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGA
32015 TTCGCCATTACAACTTCAATCTTTCCCATCATG
66 TTCGCCATTACAACTTCAATCTTTCCCATCATG
* * * *
32048 TCCCTAAGGTACAAGGTTTGCCGTTACGACTTCAACCTTTCCCTCTATATCTC
1 TCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTC
32101 TAGGGTATTA
Statistics
Matches: 210, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
97 85 0.40
98 125 0.60
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.35
Consensus pattern (98 bp):
TCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGA
TTCGCCATTACAACTTCAATCTTTCCCATCATG
Found at i:32135 original size:195 final size:195
Alignment explanation
Indices: 31750--32107 Score: 466
Period size: 195 Copynumber: 1.8 Consensus size: 195
31740 ATCTTTCCTT
* * * * * *
31750 TCACATCTCTAGGGTATAAGGTTTGCCGTTACGGCTTCAACCTTTCCCTCTATATCTTCATGGTA
1 TCACATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCACGGTA
* * ** * * * * *
31815 CAAGATTCGTCTTTACGGCTTTAATCTTTCCCATCACTTCTCTAATGTACAAGGTTCGTCGTTGC
66 CAAGATTCGCCATTACAACTTCAATCTTTCCCATCACTTCCCTAAGGTACAAGGTTCGCCGTTAC
* * * * *
31880 GGCTTCAACCTTTCCCTCCATGTCTCTATGGTACAAGATTCGCTGTTACAAATTCAATCTTCCCA
131 GACTTCAACCTTTCCCTCCATATCTCTAGGGTACAAGATTCGCCGTTACAAATCCAATCTTCCCA
* ** *
31945 TCACGTCTCTAAGGTACAAGGTTCGTTGTTACGGCTTTAACCTTTCCCTCCATATCTCCACGGTA
1 TCACATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCACGGTA
*
32010 CAAGATTCGCCATTACAACTTCAATCTTTCCCATCA-TGTCCCTAAGGTACAAGGTTTGCCGTTA
66 CAAGATTCGCCATTACAACTTCAATCTTTCCCATCACT-TCCCTAAGGTACAAGGTTCGCCGTTA
*
32074 CGACTTCAACCTTTCCCTCTATATCTCTAGGGTA
130 CGACTTCAACCTTTCCCTCCATATCTCTAGGGTA
32108 TTATATTTGC
Statistics
Matches: 138, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
194 1 0.01
195 137 0.99
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (195 bp):
TCACATCTCTAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCCATATCTCCACGGTA
CAAGATTCGCCATTACAACTTCAATCTTTCCCATCACTTCCCTAAGGTACAAGGTTCGCCGTTAC
GACTTCAACCTTTCCCTCCATATCTCTAGGGTACAAGATTCGCCGTTACAAATCCAATCTTCCCA
Found at i:32737 original size:112 final size:111
Alignment explanation
Indices: 32531--32748 Score: 303
Period size: 112 Copynumber: 1.9 Consensus size: 111
32521 CCTTACATCG
* ** *
32531 TTAGACCACTAACTGTCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGGTGGATAAAATTA
1 TTAGACCAATAACTGTCATTTCAATGCAAAAATGCTTGAACAAAGTTGTAAGATGGATAAAATTA
*
32596 AATTTTATTAGAGGTAAAGCTTACGTGAATGAAAAGATTAAAAATCA
66 AATTTTATTAGAGGCAAAGCTTAC-TGAATGAAAAGATTAAAAATCA
* * * * *
32643 TTAGTCCAATAACTGTTATTTCAATGTAAACATGCTTGAACAAAGTTGTAAGATGGATAAAATTG
1 TTAGACCAATAACTGTCATTTCAATGCAAAAATGCTTGAACAAAGTTGTAAGATGGATAAAATTA
*
32708 AATTTTATTGGAGGCAAAGCTCGTA-TGAATGAAAAGATTAA
66 AATTTTATTAGAGGCAAAGCT--TACTGAATGAAAAGATTAA
32749 GAATAAAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
112 91 0.98
114 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (111 bp):
TTAGACCAATAACTGTCATTTCAATGCAAAAATGCTTGAACAAAGTTGTAAGATGGATAAAATTA
AATTTTATTAGAGGCAAAGCTTACTGAATGAAAAGATTAAAAATCA
Found at i:33060 original size:6 final size:6
Alignment explanation
Indices: 33051--33123 Score: 71
Period size: 6 Copynumber: 12.0 Consensus size: 6
33041 TCAACCTCTC
*
33051 CTTTTT CTTTTT CCTTCTTT -TTTTT CTTCTT CTTTTT CTTTTT C-TTTT
1 CTTTTT CTTTTT -CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33099 CTTTCTCT CTTTTT -TTTTT ATTTTT
1 CTTT-T-T CTTTTT CTTTTT CTTTTT
33124 TTGGGTGAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
5 13 0.22
6 32 0.55
7 5 0.09
8 8 0.14
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:33082 original size:15 final size:15
Alignment explanation
Indices: 33052--33117 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
33042 CAACCTCTCC
*
33052 TTTTTCTTTTTCCTTCT
1 TTTTTCTTCTT-CTT-T
*
33069 TTTTT-TTCTTCTTC
1 TTTTTCTTCTTCTTT
*
33083 TTTTTCTTTTTCTTT
1 TTTTTCTTCTTCTTT
*
33098 TCTTTCTCTCTT-TTT
1 TTTTTCT-TCTTCTTT
33113 TTTTT
1 TTTTT
33118 ATTTTTTTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
14 5 0.12
15 23 0.57
16 7 0.17
17 5 0.12
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTCTTCTTT
Found at i:38814 original size:15 final size:13
Alignment explanation
Indices: 38783--38820 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
38773 CGCTAGACTC
38783 TTCTTCTTCC-TT
1 TTCTTCTTCCTTT
38795 TTCTTCTTCCTTT
1 TTCTTCTTCCTTT
38808 CTCTCTTCTTCCT
1 -T-TCTTCTTCCT
38821 CATCTTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCTTCTTCCTTT
Found at i:43607 original size:53 final size:54
Alignment explanation
Indices: 43522--43629 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 54
43512 CATTGTCACC
*
43522 AAGGAAGACATATTTCAAATGCATAGGCAAAGGCTTCAACTCCAAGGTAGGAGCT
1 AAGGAAGACA-ATTTCAAATGCATAGGCAAAGGCTTCAACGCCAAGGTAGGAGCT
* *
43577 AAGGAAGAC-ATTTCAAATGCATCGGTAAAGGCTTCAACGCCAAGGTAGGAGCT
1 AAGGAAGACAATTTCAAATGCATAGGCAAAGGCTTCAACGCCAAGGTAGGAGCT
43630 TGCTCAATAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 41 0.82
55 9 0.18
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (54 bp):
AAGGAAGACAATTTCAAATGCATAGGCAAAGGCTTCAACGCCAAGGTAGGAGCT
Found at i:46332 original size:17 final size:19
Alignment explanation
Indices: 46310--46346 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
46300 TTAAAAATCT
46310 GAAAAAGAA-AACA-ATTA
1 GAAAAAGAACAACAGATTA
*
46327 GAAAAATAACAACAGATTA
1 GAAAAAGAACAACAGATTA
46346 G
1 G
46347 TAAAGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.65, C:0.08, G:0.14, T:0.14
Consensus pattern (19 bp):
GAAAAAGAACAACAGATTA
Found at i:49628 original size:103 final size:102
Alignment explanation
Indices: 49515--49704 Score: 281
Period size: 103 Copynumber: 1.9 Consensus size: 102
49505 AGAACATTTA
* ** *
49515 TCGATTTTAAATAGGATATTTGACTACTTAGGTTCAAAGAAAAATCATACCCAGTACATTTGAGC
1 TCGATTTTAAATAGGATATTCGACTACTTAGGTTCAAAGAAAAATCATACCCAACACATTAGAGC
* *
49580 ACAATTTCTCGAGTTCCTTAAATATAGAAACATTGCC
66 ACAATTTCTCGAATTCCCTAAATATAGAAACATTGCC
* * * *
49617 TCGATTTTTAAATAGGATATTCGATTACTTAGGTTTAAAGATAAATCATACCCAACACGTTAGAG
1 TCGA-TTTTAAATAGGATATTCGACTACTTAGGTTCAAAGAAAAATCATACCCAACACATTAGAG
49682 CACAATTTCTCGAATTCCCTAAA
65 CACAATTTCTCGAATTCCCTAAA
49705 ATAAAAGAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 4 0.05
103 73 0.95
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (102 bp):
TCGATTTTAAATAGGATATTCGACTACTTAGGTTCAAAGAAAAATCATACCCAACACATTAGAGC
ACAATTTCTCGAATTCCCTAAATATAGAAACATTGCC
Found at i:51664 original size:18 final size:18
Alignment explanation
Indices: 51637--51679 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
51627 AAAATGGACC
51637 TTGG-TTTATTATTTATT
1 TTGGTTTTATTATTTATT
* * *
51654 TTTGTTTTATTTTTTGTT
1 TTGGTTTTATTATTTATT
51672 TTGGTTTT
1 TTGGTTTT
51680 TGGTTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.09, C:0.00, G:0.14, T:0.77
Consensus pattern (18 bp):
TTGGTTTTATTATTTATT
Found at i:51669 original size:12 final size:12
Alignment explanation
Indices: 51648--51690 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
51638 TGGTTTATTA
51648 TTTA-TTTTTGT
1 TTTATTTTTTGT
51659 TTTATTTTTTGT
1 TTTATTTTTTGT
** *
51671 TTTGGTTTTTGG
1 TTTATTTTTTGT
51683 TTTATTTT
1 TTTATTTT
51691 GTACTAGGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79
Consensus pattern (12 bp):
TTTATTTTTTGT
Found at i:54668 original size:41 final size:40
Alignment explanation
Indices: 54608--54852 Score: 144
Period size: 38 Copynumber: 6.2 Consensus size: 40
54598 GTACAAGTTA
* * *
54608 CCTGATACAATACATCGGCACGAAACTTGCTAGGCTCAAAG
1 CCTGATA-AATACACCGGCACGAAACCTGCTAGGCACAAAG
* * *
54649 CCTGATAATATACACCGGCATGAAGCCTGCTAGGCACTAAG
1 CCTGATAA-ATACACCGGCACGAAACCTGCTAGGCACAAAG
* * ** * * ***
54690 CCTGATAAATGCACCGACATAAAAACTGTTAGGCATTGAG
1 CCTGATAAATACACCGGCACGAAACCTGCTAGGCACAAAG
* * * * **
54730 CCCGAT-AA-ACATCGGTACGAATCCTGCTAGGCACTGAG
1 CCTGATAAATACACCGGCACGAAACCTGCTAGGCACAAAG
* * * **
54768 CCTGAT-AA-ACATCGGTACGAATCCTGCTAGGCACTGAG
1 CCTGATAAATACACCGGCACGAAACCTGCTAGGCACAAAG
* * *
54806 CCTGAT-AA-ACATCGGCAC-AAAGCTTGCTAGGCACTAAG
1 CCTGATAAATACACCGGCACGAAA-CCTGCTAGGCACAAAG
*
54844 CCCGATAAA
1 CCTGATAAA
54853 CACCACGTAC
Statistics
Matches: 170, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
37 2 0.01
38 93 0.55
39 4 0.02
40 30 0.18
41 41 0.24
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (40 bp):
CCTGATAAATACACCGGCACGAAACCTGCTAGGCACAAAG
Found at i:54723 original size:40 final size:40
Alignment explanation
Indices: 54630--54738 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
54620 CATCGGCACG
* * * *
54630 AAACTTGCTAGGCTCAAAGCCTGATAATATACACCGGCATGA
1 AAAC-TGCTAGGCACTAAGCCTGATAA-ATACACCGACATAA
** *
54672 AGCCTGCTAGGCACTAAGCCTGATAAATGCACCGACATAA
1 AAACTGCTAGGCACTAAGCCTGATAAATACACCGACATAA
* * * *
54712 AAACTGTTAGGCATTGAGCCCGATAAA
1 AAACTGCTAGGCACTAAGCCTGATAAA
54739 CATCGGTACG
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 32 0.59
41 20 0.37
42 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
AAACTGCTAGGCACTAAGCCTGATAAATACACCGACATAA
Found at i:54768 original size:38 final size:38
Alignment explanation
Indices: 54719--54854 Score: 200
Period size: 38 Copynumber: 3.6 Consensus size: 38
54709 TAAAAACTGT
*
54719 TAGGCATTGAGCCCGATAAACATCGGTACGAATCCTGC
1 TAGGCACTGAGCCCGATAAACATCGGTACGAATCCTGC
*
54757 TAGGCACTGAGCCTGATAAACATCGGTACGAATCCTGC
1 TAGGCACTGAGCCCGATAAACATCGGTACGAATCCTGC
* * * * *
54795 TAGGCACTGAGCCTGATAAACATCGGCACAAAGCTTGC
1 TAGGCACTGAGCCCGATAAACATCGGTACGAATCCTGC
*
54833 TAGGCACTAAGCCCGATAAACA
1 TAGGCACTGAGCCCGATAAACA
54855 CCACGTACAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 90 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (38 bp):
TAGGCACTGAGCCCGATAAACATCGGTACGAATCCTGC
Found at i:58725 original size:20 final size:19
Alignment explanation
Indices: 58700--58740 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
58690 ATTTCATACA
*
58700 TTGCATTTAGGTTAATTCAT
1 TTGCATTTA-GTTAATTAAT
58720 TTGCATTTAGTTAATTAAT
1 TTGCATTTAGTTAATTAAT
58739 TT
1 TT
58741 AATTTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (19 bp):
TTGCATTTAGTTAATTAAT
Found at i:61502 original size:25 final size:25
Alignment explanation
Indices: 61468--61517 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
61458 GGATAAATCT
61468 GTTCTCCCAATATGATCCTATTTTA
1 GTTCTCCCAATATGATCCTATTTTA
61493 GTTCTCCCAATATGATCCTATTTTA
1 GTTCTCCCAATATGATCCTATTTTA
61518 TCTCATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (25 bp):
GTTCTCCCAATATGATCCTATTTTA
Found at i:69472 original size:61 final size:58
Alignment explanation
Indices: 69398--69530 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 58
69388 TCCAAAAATA
* * * ** *
69398 ATATTATTTTAATAGTTTTAATATTAAATTAAATTTAATATTTATCTTGTAAATAAATATT
1 ATATTAATTTAATAGATTTAATATCAAATTAAACCTAACATTTATCTTG---ATAAATATT
* *
69459 ATATTAATTTAATAGATTTAATATCAAATTTAACCTAACATTTATCTTGATAAGTATT
1 ATATTAATTTAATAGATTTAATATCAAATTAAACCTAACATTTATCTTGATAAATATT
69517 ATATTAATTTAATA
1 ATATTAATTTAATA
69531 TTAAAGTGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 22 0.34
61 42 0.66
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.49
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATCAAATTAAACCTAACATTTATCTTGATAAATATT
Found at i:69482 original size:20 final size:20
Alignment explanation
Indices: 69396--69482 Score: 56
Period size: 20 Copynumber: 4.3 Consensus size: 20
69386 ATTCCAAAAA
* *
69396 TAATATTATTTTAATAGTTT
1 TAATATTAATTTAATAGATT
*
69416 TAATATTAAATT-A-A-ATT
1 TAATATTAATTTAATAGATT
* *
69433 TAATATTTATCTTGTAAATAAATAT
1 TAATA-TTA-ATT-T-AATAGAT-T
69458 T-ATATTAATTTAATAGATT
1 TAATATTAATTTAATAGATT
69477 TAATAT
1 TAATAT
69483 CAAATTTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
17 7 0.14
18 4 0.08
19 4 0.08
20 21 0.41
21 1 0.02
22 3 0.06
23 4 0.08
24 5 0.10
25 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (20 bp):
TAATATTAATTTAATAGATT
Found at i:71223 original size:18 final size:19
Alignment explanation
Indices: 71192--71250 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
71182 TAATTATTAG
*
71192 AAATAAATTAAAAACCATA
1 AAATTAATTAAAAACCATA
* * *
71211 AAATTTA-TAAAAA-TAAA
1 AAATTAATTAAAAACCATA
71228 TAAATTAATTAAAAACCATA
1 -AAATTAATTAAAAACCATA
71248 AAA
1 AAA
71251 ATAGAAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
17 2 0.07
18 12 0.40
19 14 0.47
20 2 0.07
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATTAATTAAAAACCATA
Found at i:71338 original size:10 final size:10
Alignment explanation
Indices: 71296--71343 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
71286 ATTAAAAACC
71296 ATAAAATTTT
1 ATAAAATTTT
* **
71306 ATAATAAATAA
1 ATAA-AATTTT
71317 ATAAATATTTT
1 ATAAA-ATTTT
71328 ATAAAATTTT
1 ATAAAATTTT
71338 ATAAAA
1 ATAAAA
71344 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
10 16 0.53
11 14 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAAAATTTT
Found at i:71888 original size:39 final size:41
Alignment explanation
Indices: 71797--71889 Score: 95
Period size: 41 Copynumber: 2.3 Consensus size: 41
71787 TTTTTCTAAA
* * *
71797 TTTTTATGATTTTTAATAAATTATTTTTATAAATTTTATTG
1 TTTTTATAATTTCTAATAAATTATTTATATAAATTTTATTG
*
71838 TTTTAATTAATTTCTAAT-AATTA-TTATA-AAATTTAATATT-
1 TTTTTA-TAATTTCTAATAAATTATTTATATAAATTT--TATTG
71878 TTTTTATAATTT
1 TTTTTATAATTT
71890 TTTATTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
39 12 0.27
40 9 0.20
41 14 0.32
42 9 0.20
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (41 bp):
TTTTTATAATTTCTAATAAATTATTTATATAAATTTTATTG
Found at i:71892 original size:10 final size:10
Alignment explanation
Indices: 71877--71909 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
71867 AATTTAATAT
71877 TTTTTTATAA
1 TTTTTTATAA
*
71887 TTTTTTAT-T
1 TTTTTTATAA
71896 TTTTTTATAA
1 TTTTTTATAA
71906 TTTT
1 TTTT
71910 AAAATGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:78637 original size:2 final size:2
Alignment explanation
Indices: 78630--78698 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
78620 CTTCTTTTTA
* * *
78630 AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
78672 AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
78699 GGGAGAGAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:80296 original size:295 final size:297
Alignment explanation
Indices: 79763--80357 Score: 1122
Period size: 295 Copynumber: 2.0 Consensus size: 297
79753 GCTCGTGTGT
79763 GAGAGATAGATCAACTTGCCCACTAGTCTTTGATACTGCCCTTTATCCACTGGTGCACTCTCCTC
1 GAGAGATAGATCAACTTGCCCACTAGTCTTTGATACTGCCCTTTATCCACTGGTGCAC-CTCCTC
*
79828 ATATTTCCTTAATTTTAAGTTTGGGTCCATAGGCGTCTTTGCAGGTTTACACCCAAGCATGCAAG
65 ATATTTCCTTAATTTTAAGTTTGGGTCCATAGGCATCTTTGCAGGTTTACACCCAAGCATGCAAG
*
79893 TCTCAGTTAGCAAATCTAAGATGTTTCTTTGGGATATAACAATACTTGCCTTAGTTCGAGCAACC
130 TCTCAGTTAGCAAATCTAAGATGTTTCTTTGGGATATAACAATACCTGCCTTAGTTCGAGCAACC
79958 TCCATGCCTAGGAAATATTTGACAGCGTCAAGATCTTTAATTTCAAACTCAGTAGCAAGTAATTT
195 TCCATGCCTAGGAAATATTTGACAGCGTCAAGATCTTTAATTTCAAACTCAGTAGCAAGTAATTT
80023 TTTGAGTTTGATAATCTCTTCTAAGTCATCACCAATTA
260 TTTGAGTTTGATAATCTCTTCTAAGTCATCACCAATTA
*
80061 GAGAGATAGATCAACTTGCCCACTAGTCTTTGCTACTGCCCTTTATCCACTGGTGCA-CT-CTCA
1 GAGAGATAGATCAACTTGCCCACTAGTCTTTGATACTGCCCTTTATCCACTGGTGCACCTCCTCA
80124 TATTTCCTTAATTTTAAGTTTGGGTCCATAGGCATCTTTGCAGGTTTACACCCAAGCATGCAAGT
66 TATTTCCTTAATTTTAAGTTTGGGTCCATAGGCATCTTTGCAGGTTTACACCCAAGCATGCAAGT
80189 CTCAGTTAGCAAATCTAAGATGTTTCTTTGGGATATAACAATACCTGCCTTAGTTCGAGCAACCT
131 CTCAGTTAGCAAATCTAAGATGTTTCTTTGGGATATAACAATACCTGCCTTAGTTCGAGCAACCT
* *
80254 TCATGCCTAGGAAATATTTGAGAGCGTCAAGATCTTTAATTTCAAACTCAGTAGCAAGTAATTTT
196 CCATGCCTAGGAAATATTTGACAGCGTCAAGATCTTTAATTTCAAACTCAGTAGCAAGTAATTTT
80319 TTGAGTTTGATAATCTCTTCTAAGTCATCACCAATTA
261 TTGAGTTTGATAATCTCTTCTAAGTCATCACCAATTA
80356 GA
1 GA
80358 ATGATGTCGT
Statistics
Matches: 292, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
295 234 0.80
296 2 0.01
298 56 0.19
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (297 bp):
GAGAGATAGATCAACTTGCCCACTAGTCTTTGATACTGCCCTTTATCCACTGGTGCACCTCCTCA
TATTTCCTTAATTTTAAGTTTGGGTCCATAGGCATCTTTGCAGGTTTACACCCAAGCATGCAAGT
CTCAGTTAGCAAATCTAAGATGTTTCTTTGGGATATAACAATACCTGCCTTAGTTCGAGCAACCT
CCATGCCTAGGAAATATTTGACAGCGTCAAGATCTTTAATTTCAAACTCAGTAGCAAGTAATTTT
TTGAGTTTGATAATCTCTTCTAAGTCATCACCAATTA
Found at i:86312 original size:7 final size:7
Alignment explanation
Indices: 86278--86312 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
86268 GGAGGTTTGA
*
86278 TTTGGAA
1 TTTGGAC
*
86285 TTTGGAA
1 TTTGGAC
86292 TTTGGAC
1 TTTGGAC
86299 TTTGGAC
1 TTTGGAC
86306 TTTGGAC
1 TTTGGAC
86313 CCTTTGGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.43
Consensus pattern (7 bp):
TTTGGAC
Found at i:88847 original size:39 final size:40
Alignment explanation
Indices: 88794--88873 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
88784 AAGAGGTATG
* *
88794 TCCAATATGAAAAGGATTGTGACTCTTCAATAGATGTCCA
1 TCCAATATGAAAAGGATTCTGACTCTTCAAAAGATGTCCA
* * *
88834 TCCAATTTG-AAAGGGTTCTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTCTGACTCTTCAAAAGATGTCCA
88873 T
1 T
88874 TAAGTGCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTCTGACTCTTCAAAAGATGTCCA
Found at i:94246 original size:20 final size:21
Alignment explanation
Indices: 94221--94275 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
94211 ATGGGCCCAA
94221 ACTATTGATACAAATAGGG-T
1 ACTATTGATACAAATAGGGCT
* *
94241 ACTATTGATACTATTAGGGCT
1 ACTATTGATACAAATAGGGCT
*
94262 ACTATTGAAACAAA
1 ACTATTGATACAAA
94276 GTCATTTCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (21 bp):
ACTATTGATACAAATAGGGCT
Found at i:101511 original size:7 final size:7
Alignment explanation
Indices: 101501--101531 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
101491 CTCACCAAAA
*
101501 TCATCCT
1 TCATCCC
101508 TCATCCC
1 TCATCCC
101515 TCATCCC
1 TCATCCC
101522 TCATCCC
1 TCATCCC
101529 TCA
1 TCA
101532 CTTCACATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (7 bp):
TCATCCC
Found at i:103632 original size:45 final size:45
Alignment explanation
Indices: 103524--103632 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 45
103514 AGTAAATGAT
103524 TAAGACCATAGTTGAAAGACATTATGACACTATATTGAGAATAAA
1 TAAGACCATAGTTGAAAGACATTATGACACTATATTGAGAATAAA
* *
103569 TAAGACCATAGTCGAAAGACATTATGGCA-TCA-AGTTGAGAATAAA
1 TAAGACCATAGTTGAAAGACATTATGACACT-ATA-TTGAGAATAAA
* *
103614 TAAGACCATGGTTTAAAGA
1 TAAGACCATAGTTGAAAGA
103633 TACCATGGCA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 2 0.04
45 55 0.96
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACATTATGACACTATATTGAGAATAAA
Found at i:105609 original size:20 final size:20
Alignment explanation
Indices: 105584--105840 Score: 206
Period size: 20 Copynumber: 12.8 Consensus size: 20
105574 TAGATCAATA
*
105584 TGTTTGCACCTCGATGCCCT
1 TGTTTGCACTTCGATGCCCT
*
105604 TGTTTGCACTACGATG-CCT
1 TGTTTGCACTTCGATGCCCT
*
105623 CTGTTTGCACTTCGGTG-CCT
1 -TGTTTGCACTTCGATGCCCT
* *
105643 CTGTTTGCACTTCGGTGCCCC
1 -TGTTTGCACTTCGATGCCCT
* *
105664 TATTTGCACTTCGATGCCCC
1 TGTTTGCACTTCGATGCCCT
* * *
105684 TATTTGCAATTCGATGCCCC
1 TGTTTGCACTTCGATGCCCT
*
105704 TGTTTGCACTTTGATGCCCCT
1 TGTTTGCACTTCGATG-CCCT
*
105725 T-TTTGCACTACGATG-CCT
1 TGTTTGCACTTCGATGCCCT
*
105743 CTGTTTGCACTTC-ACTGCCCC
1 -TGTTTGCACTTCGA-TGCCCT
* * *
105764 TATTTACACTAC-AGTG-CCT
1 TGTTTGCACTTCGA-TGCCCT
* *
105783 CTGTTTGCACTACGGTGCCCT
1 -TGTTTGCACTTCGATGCCCT
* *
105804 TGTTTGCACTTTGGTGCCGC-
1 TGTTTGCACTTCGATGCC-CT
105824 TGTTTGCACTTCGATGC
1 TGTTTGCACTTCGATGC
105841 TCCTAAATGC
Statistics
Matches: 198, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.02
19 7 0.04
20 176 0.89
21 12 0.06
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (20 bp):
TGTTTGCACTTCGATGCCCT
Found at i:105648 original size:40 final size:40
Alignment explanation
Indices: 105584--105840 Score: 275
Period size: 40 Copynumber: 6.4 Consensus size: 40
105574 TAGATCAATA
* *
105584 TGTTTGCACCTCGATGCCCTTGTTTGCACTACGATGCCTC
1 TGTTTGCACTTCGATGCCCCTGTTTGCACTACGATGCCTC
* * * * *
105624 TGTTTGCACTTCGGTGCCTCTGTTTGCACTTCGGTGCCCC
1 TGTTTGCACTTCGATGCCCCTGTTTGCACTACGATGCCTC
* * * * *
105664 TATTTGCACTTCGATGCCCCTATTTGCAATTCGATGCCCC
1 TGTTTGCACTTCGATGCCCCTGTTTGCACTACGATGCCTC
* *
105704 TGTTTGCACTTTGATGCCCCTTTTTGCACTACGATGCCTC
1 TGTTTGCACTTCGATGCCCCTGTTTGCACTACGATGCCTC
* *
105744 TGTTTGCACTTC-ACTGCCCCTATTTACACTAC-AGTGCCTC
1 TGTTTGCACTTCGA-TGCCCCTGTTTGCACTACGA-TGCCTC
* * * ** * *
105784 TGTTTGCACTACGGTGCCCTTGTTTGCACTTTGGTGCCGC
1 TGTTTGCACTTCGATGCCCCTGTTTGCACTACGATGCCTC
105824 TGTTTGCACTTCGATGC
1 TGTTTGCACTTCGATGC
105841 TCCTAAATGC
Statistics
Matches: 180, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.01
40 178 0.99
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (40 bp):
TGTTTGCACTTCGATGCCCCTGTTTGCACTACGATGCCTC
Found at i:105852 original size:60 final size:60
Alignment explanation
Indices: 105584--105845 Score: 285
Period size: 60 Copynumber: 4.4 Consensus size: 60
105574 TAGATCAATA
* * * *
105584 TGTTTGCACCTCGATGCCCTTGTTTGCACTACGATGCCTCTGTTTGCACTTCGGTGCCTC
1 TGTTTGCACTTCGATGCCCCTATTTGCACTACGATGCCTCTGTTTGCACTTCGGTGCCCC
* * * * * *
105644 TGTTTGCACTTCGGTGCCCCTATTTGCACTTCGATGCCCCTATTTGCAATTCGATGCCCC
1 TGTTTGCACTTCGATGCCCCTATTTGCACTACGATGCCTCTGTTTGCACTTCGGTGCCCC
* * **
105704 TGTTTGCACTTTGATGCCCCTTTTTGCACTACGATGCCTCTGTTTGCACTTCACTGCCCC
1 TGTTTGCACTTCGATGCCCCTATTTGCACTACGATGCCTCTGTTTGCACTTCGGTGCCCC
* * * * * * * *
105764 TATTTACACTAC-AGTGCCTCTGTTTGCACTACGGTGCC-CTTGTTTGCACTTTGGTGCCGC
1 TGTTTGCACTTCGA-TGCCCCTATTTGCACTACGATGCCTC-TGTTTGCACTTCGGTGCCCC
*
105824 TGTTTGCACTTCGATGCTCCTA
1 TGTTTGCACTTCGATGCCCCTA
105846 AATGCACAAT
Statistics
Matches: 163, Mismatches: 36, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
59 2 0.01
60 160 0.98
61 1 0.01
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.37
Consensus pattern (60 bp):
TGTTTGCACTTCGATGCCCCTATTTGCACTACGATGCCTCTGTTTGCACTTCGGTGCCCC
Found at i:107209 original size:2 final size:2
Alignment explanation
Indices: 107202--107234 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
107192 ACCAAGTTAA
107202 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
107235 AGTTCAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:111839 original size:132 final size:132
Alignment explanation
Indices: 111597--111842 Score: 341
Period size: 132 Copynumber: 1.9 Consensus size: 132
111587 TACATAGGTG
*
111597 CTGGTCTTAGATGTCCTACCGATGTCTGAGATCCAACATTTATTGCAGATTCTCCATAGCTCGTG
1 CTGGTCTTAGATGTCCTACCGATGTCTGAGATCCAACATTTATTGCAGATTCTCCACAGCTCGTG
* * * * * *
111662 TCAGTAGCATTGTGTAGGTCAACATCTCGACCCACAACTCGTGTGAGCATTACATGTTATATGGA
66 TAAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACACATGTGAGCATTACATGTTATATGGA
111727 TA
131 TA
**** **
111729 CTGGTCTTAGATGTCCTACCGATTGT-TGAGATTTGTCATTTATTGTGGATTCTCCACAGCTCGT
1 CTGGTCTTAGATGTCCTACCGA-TGTCTGAGATCCAACATTTATTGCAGATTCTCCACAGCTCGT
* *
111793 GTAAGCAGCATCGTGTAGCTCAACATCTTGACCCACAGCACATGTGAGCA
65 GTAAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACACATGTGAGCA
111843 GGCCCATTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
132 95 0.97
133 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (132 bp):
CTGGTCTTAGATGTCCTACCGATGTCTGAGATCCAACATTTATTGCAGATTCTCCACAGCTCGTG
TAAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACACATGTGAGCATTACATGTTATATGGA
TA
Found at i:114873 original size:21 final size:19
Alignment explanation
Indices: 114824--114879 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
114814 GAATAATGTA
114824 GACTTCTACCGATACAAGT
1 GACTTCTACCGATACAAGT
114843 GACTTTCTACCGATACAAGTCT
1 GAC-TTCTACCGATACAAG--T
*
114865 TACTTCTACCGATAC
1 GACTTCTACCGATAC
114880 TAAAAACTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 12 0.36
22 3 0.09
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (19 bp):
GACTTCTACCGATACAAGT
Found at i:123303 original size:21 final size:21
Alignment explanation
Indices: 123277--123336 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
123267 AATAGTACAG
*
123277 ACTTCTACCGATACAAGTGAC
1 ACTTCTATCGATACAAGTGAC
*
123298 AGTTCTATCGATACAAGTGAC
1 ACTTCTATCGATACAAGTGAC
*
123319 TCTTCTATCGATACAAGT
1 ACTTCTATCGATACAAGT
123337 CTTACTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (21 bp):
ACTTCTATCGATACAAGTGAC
Found at i:126707 original size:26 final size:26
Alignment explanation
Indices: 126633--126705 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
126623 AAAACTATTC
*
126633 TAAAATAAAACTCAAGAGAAATTCTA
1 TAAAAGAAAACTCAAGAGAAATTCTA
*
126659 TAAAAGAAAACTCAAGAGAAATTCTT
1 TAAAAGAAAACTCAAGAGAAATTCTA
*
126685 TAAAAGAAAACTAAAAGAGAA
1 TAAAAGAAAACT-CAAGAGAA
126706 TTTTATTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
26 36 0.84
27 7 0.16
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (26 bp):
TAAAAGAAAACTCAAGAGAAATTCTA
Found at i:126714 original size:27 final size:27
Alignment explanation
Indices: 126633--126714 Score: 107
Period size: 26 Copynumber: 3.1 Consensus size: 27
126623 AAAACTATTC
*
126633 TAAAATAAAACTCAAGAGAAATTCTA-
1 TAAAAGAAAACTCAAGAGAAATTCTAT
126659 TAAAAGAAAACTCAAGAGAAATTCT-T
1 TAAAAGAAAACTCAAGAGAAATTCTAT
* *
126685 TAAAAGAAAACT-AAAAGAGAATTTTAT
1 TAAAAGAAAACTCAAGAGA-AATTCTAT
126712 TAA
1 TAA
126715 CTGAAAAACA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
25 5 0.10
26 41 0.82
27 4 0.08
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (27 bp):
TAAAAGAAAACTCAAGAGAAATTCTAT
Found at i:129803 original size:50 final size:49
Alignment explanation
Indices: 129720--129847 Score: 134
Period size: 50 Copynumber: 2.6 Consensus size: 49
129710 TGCATGACTT
*
129720 GATTTAATGATGC-ATTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAATTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * *
129769 GATTTATGATGCATATTTAACTAACATGTAAGTTACTTAATGCTTGTCAT
1 GATTTATGATGCA-ATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
129819 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGC-AATTTAACTAA-CATG
129848 AGAGTTAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
48 7 0.10
49 6 0.09
50 49 0.73
51 5 0.07
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (49 bp):
GATTTATGATGCAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:130080 original size:17 final size:17
Alignment explanation
Indices: 130049--130081 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
130039 CAAACACTTA
130049 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
130066 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
130082 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:132200 original size:16 final size:16
Alignment explanation
Indices: 132164--132215 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
132154 GATAAATATC
*
132164 ATAAACTAAATAACTAAA
1 ATAAA-TAAACAAC-AAA
132182 ATAAATAAACAACAAA
1 ATAAATAAACAACAAA
* *
132198 ATAAAAAAACAACTAA
1 ATAAATAAACAACAAA
132214 AT
1 AT
132216 CAATTAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 19 0.61
17 7 0.23
18 5 0.16
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (16 bp):
ATAAATAAACAACAAA
Found at i:145083 original size:15 final size:16
Alignment explanation
Indices: 145052--145089 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
145042 AAAAAAATAA
*
145052 TCAAAATTTACAAGTC
1 TCAAAAATTACAAGTC
145068 TCAAAAATTA-AAGTC
1 TCAAAAATTACAAGTC
*
145083 TTAAAAA
1 TCAAAAA
145090 CACTTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (16 bp):
TCAAAAATTACAAGTC
Found at i:145791 original size:22 final size:22
Alignment explanation
Indices: 145766--145814 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
145756 TCTTTGTCGT
*
145766 GACATGAAGAGAGCTATGTCAC
1 GACATAAAGAGAGCTATGTCAC
145788 GACATAAAGAGAGCTATGTCAC
1 GACATAAAGAGAGCTATGTCAC
145810 GACAT
1 GACAT
145815 CGACATCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (22 bp):
GACATAAAGAGAGCTATGTCAC
Found at i:155083 original size:15 final size:15
Alignment explanation
Indices: 155063--155094 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
155053 CCAGATGAAG
*
155063 GAGAAGGAAGAGGAA
1 GAGAAGGAAGAGAAA
155078 GAGAAGGAAGAGAAA
1 GAGAAGGAAGAGAAA
155093 GA
1 GA
155095 AAAAGAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (15 bp):
GAGAAGGAAGAGAAA
Found at i:155445 original size:24 final size:24
Alignment explanation
Indices: 155400--155445 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
155390 AGTTTGACGA
* *
155400 ATAAAAAAAGGAAGAGGTACAAAG
1 ATAAAAAAAGGAAGAAGCACAAAG
155424 ATAAAAAGAA-GAAGAAGCACAA
1 ATAAAAA-AAGGAAGAAGCACAA
155446 GGAAAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.65, C:0.07, G:0.22, T:0.07
Consensus pattern (24 bp):
ATAAAAAAAGGAAGAAGCACAAAG
Found at i:156198 original size:12 final size:11
Alignment explanation
Indices: 156169--156218 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
156159 CAGTCAATTG
156169 AAAA-AGAAAA
1 AAAAGAGAAAA
*
156179 AAATGAGAAAA
1 AAAAGAGAAAA
156190 AGAAAGAGAAAA
1 A-AAAGAGAAAA
156202 TAAAAGAAGAAAA
1 -AAAAG-AGAAAA
156215 AAAA
1 AAAA
156219 ATTATTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 3 0.09
11 7 0.21
12 17 0.50
13 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:160240 original size:51 final size:51
Alignment explanation
Indices: 160164--160407 Score: 332
Period size: 51 Copynumber: 4.8 Consensus size: 51
160154 GAAAGAGTTT
* * *
160164 GATGACTAAGTGTCATCGTGGGTAAACGAATCCTTTACGGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTCC
160215 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTCC
* *
160266 GATGACTAAGTGTCATCGTGAGTAAATGAATCATCTACGGATTAAAGGTCT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTCC
* * * **
160317 GATGACT-AGTGTCATTGTGAGTAAATGAATCCAT-GACGAATTAAAGGTTT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCC-TCTACGGATTAAAGGTCC
* * *
160367 GATGACTCAA-TGTCATCGTGAGTATATGAATTCTATACGGA
1 GATGACT-AAGTGTCATCGTGAGTAAATGAATCCTCTACGGA
160408 ACAAGGGGGC
Statistics
Matches: 174, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
50 44 0.25
51 129 0.74
52 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTCC
Found at i:160387 original size:101 final size:102
Alignment explanation
Indices: 160155--160397 Score: 339
Period size: 101 Copynumber: 2.4 Consensus size: 102
160145 GCTATAAACG
* * * *
160155 AAAGAGTTTGATGACTAAGTGTCATCGTGGGTAAACGAATCCTTTACGGATTAAAGGTCCGATGA
1 AAAG-GTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCATCTACGGATTAAAGGTCCGATGA
* *
160220 CTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATT
65 CTAAGTGTCATCGTGAGTAAATGAATCCTCGACGAATT
** *
160258 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATCTACGGATTAAAGGTCTGATGAC
1 AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCATCTACGGATTAAAGGTCCGATGAC
*
160323 T-AGTGTCATTGTGAGTAAATGAATCCAT-GACGAATT
66 TAAGTGTCATCGTGAGTAAATGAATCC-TCGACGAATT
*
160359 AAAGGTTTGATGACTCAA-TGTCATCGTGAGTATATGAAT
1 AAAGGTTTGATGACT-AAGTGTCATCGTGAGTAAATGAAT
160398 TCTATACGGA
Statistics
Matches: 125, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
101 63 0.50
102 58 0.46
103 4 0.03
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (102 bp):
AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCATCTACGGATTAAAGGTCCGATGAC
TAAGTGTCATCGTGAGTAAATGAATCCTCGACGAATT
Found at i:161569 original size:51 final size:51
Alignment explanation
Indices: 161505--161739 Score: 314
Period size: 51 Copynumber: 4.6 Consensus size: 51
161495 CTATAAACAA
* * * *
161505 AAAGGTCCAATGACTAAGTGTCATCGTGGGTAAACAAATCCAT-TACGGATT
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAACGAATCC-TCTACGGATT
* *
161556 AAAGGTCCGATGACTAAGTGTCATTGTAAGTAAACGAATCCTCTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAACGAATCCTCTACGGATT
* *
161607 AAAGGTCCGATAACTAAGTGTCATTATGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAACGAATCCTCTACGGATT
* * *
161658 AAAGGTCCGATGACTAA-TGTCATTGTGAGTAAATGAATCCAT-GACGAATT
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAACGAATCC-TCTACGGATT
* *
161708 AAAGGTCCGATGACTCAGTGTCATCGTGAGTA
1 AAAGGTCCGATGACTAAGTGTCATTGTGAGTA
161740 TATGAATTTC
Statistics
Matches: 164, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
50 44 0.27
51 120 0.73
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAACGAATCCTCTACGGATT
Found at i:165487 original size:52 final size:52
Alignment explanation
Indices: 165409--165513 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
165399 TGAAGAGAAA
165409 TTGTTTACTGTCGACGCATCCTCACGGTATGCGGATGAAGTCAACTACTTGG
1 TTGTTTACTGTCGACGCATCCTCACGGTATGCGGATGAAGTCAACTACTTGG
165461 TTGTTTACTGTCGACGCATCCTCACGGTATGCGGATGAAGTCAACTACTTGG
1 TTGTTTACTGTCGACGCATCCTCACGGTATGCGGATGAAGTCAACTACTTGG
165513 T
1 T
165514 ATGTAAAAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (52 bp):
TTGTTTACTGTCGACGCATCCTCACGGTATGCGGATGAAGTCAACTACTTGG
Found at i:172753 original size:19 final size:19
Alignment explanation
Indices: 172694--172759 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
172684 TAGCTCGTTT
*
172694 GAGCAC-ACTGGCTCGTAA
1 GAGCACTACTGGCTCATAA
* * **
172712 GAGCAATACCGGCTCATTT
1 GAGCACTACTGGCTCATAA
*
172731 GAGCACTACTGTCTCATAA
1 GAGCACTACTGGCTCATAA
*
172750 GAGCATTACT
1 GAGCACTACT
172760 AGGTCGCATG
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
18 5 0.14
19 31 0.86
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (19 bp):
GAGCACTACTGGCTCATAA
Found at i:175740 original size:13 final size:12
Alignment explanation
Indices: 175696--175752 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
175686 AGTTGGTAAA
*
175696 ATGAAATGCTTAG
1 ATGAAATG-TTAT
175709 ATGAAATAGTTAT
1 ATGAAAT-GTTAT
*
175722 ACGAAATGTTATT
1 ATGAAATGTTA-T
*
175735 ATGAAACGGTTAT
1 ATGAAA-TGTTAT
175748 ATGAA
1 ATGAA
175753 GTATTTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 4 0.11
13 28 0.76
14 5 0.14
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.33
Consensus pattern (12 bp):
ATGAAATGTTAT
Found at i:176468 original size:21 final size:21
Alignment explanation
Indices: 176444--176483 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
176434 TAGAAGTCAA
176444 AGTTGTACCGATAGAACTCCT
1 AGTTGTACCGATAGAACTCCT
* *
176465 AGTTGTACTGGTAGAACTC
1 AGTTGTACCGATAGAACTC
176484 TATATCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
AGTTGTACCGATAGAACTCCT
Found at i:178939 original size:31 final size:31
Alignment explanation
Indices: 178901--178964 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
178891 ATCCATCATA
178901 CTAGCTTTGGCCCCACTAAAAATTCCTTATC
1 CTAGCTTTGGCCCCACTAAAAATTCCTTATC
178932 CTAGCTTTGGCCCCACTAAAAATTCCTTATC
1 CTAGCTTTGGCCCCACTAAAAATTCCTTATC
178963 CT
1 CT
178965 TGTCATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.09, T:0.33
Consensus pattern (31 bp):
CTAGCTTTGGCCCCACTAAAAATTCCTTATC
Found at i:184378 original size:19 final size:19
Alignment explanation
Indices: 184354--184416 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
184344 TGAAAGGAAT
184354 GCAATACTGGCTCGTAAGA
1 GCAATACTGGCTCGTAAGA
*
184373 GCAATACTGGCTCGCAAGA
1 GCAATACTGGCTCGTAAGA
* * *
184392 GCAATACTAGCTCATGAGA
1 GCAATACTGGCTCGTAAGA
184411 GCAATA
1 GCAATA
184417 TACTGTACTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (19 bp):
GCAATACTGGCTCGTAAGA
Found at i:185640 original size:101 final size:101
Alignment explanation
Indices: 185465--185668 Score: 372
Period size: 101 Copynumber: 2.0 Consensus size: 101
185455 TCTCAACAAC
* *
185465 AAAAATCAAAGGACAAAAGTAGAAGAAGACAAAATGTTTCACTATGAGCAAACAAAAAACAAGAG
1 AAAAATCAAAAGACAAAAGTAGAAGAAGACAAAATGTGTCACTATGAGCAAACAAAAAACAAGAG
185530 AAATGGTGCCATAAGGCAGACACAGAACTATTCCTT
66 AAATGGTGCCATAAGGCAGACACAGAACTATTCCTT
* *
185566 AAAAATCAAAAGACAAAAGTAGAAGAAGACAACATGTGTCACTATGAGCAAACAAAAAACGAGAG
1 AAAAATCAAAAGACAAAAGTAGAAGAAGACAAAATGTGTCACTATGAGCAAACAAAAAACAAGAG
185631 AAATGGTGCCATAAGGCAGACACAGAACTATTCCTT
66 AAATGGTGCCATAAGGCAGACACAGAACTATTCCTT
185667 AA
1 AA
185669 TTATCGTGTA
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.15
Consensus pattern (101 bp):
AAAAATCAAAAGACAAAAGTAGAAGAAGACAAAATGTGTCACTATGAGCAAACAAAAAACAAGAG
AAATGGTGCCATAAGGCAGACACAGAACTATTCCTT
Found at i:187538 original size:22 final size:19
Alignment explanation
Indices: 187508--187548 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 19
187498 ATGATTTCTG
187508 AAAAATAATTTATTTTTTTGA
1 AAAAATAA--TATTTTTTTGA
187529 AAAAATTAATATTTTTTTGA
1 AAAAA-TAATATTTTTTTGA
187549 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 5 0.26
22 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
AAAAATAATATTTTTTTGA
Found at i:203445 original size:27 final size:27
Alignment explanation
Indices: 203415--203480 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
203405 CTTATTATTT
203415 TGCTTATTACGGTTTTTGCCATTTACA
1 TGCTTATTACGGTTTTTGCCATTTACA
*
203442 TGCTTATTACGGTTTTTGCCGTTTACA
1 TGCTTATTACGGTTTTTGCCATTTACA
203469 TGCTTATTACGG
1 TGCTTATTACGG
203481 ACGGGCAGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (27 bp):
TGCTTATTACGGTTTTTGCCATTTACA
Found at i:205449 original size:8 final size:9
Alignment explanation
Indices: 205428--205479 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
205418 TTCTACAAAG
205428 AAAAACATT
1 AAAAACATT
205437 AAAAACATT
1 AAAAACATT
**
205446 AAAAA-AAA
1 AAAAACATT
205454 AAAATACATTT
1 AAAA-ACA-TT
205465 AAAATACATT
1 AAAA-ACATT
205475 AAAAA
1 AAAAA
205480 TTCTTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 5 0.14
9 16 0.44
10 7 0.19
11 8 0.22
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAACATT
Found at i:205622 original size:21 final size:21
Alignment explanation
Indices: 205598--205687 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 21
205588 AAAAACACCC
*
205598 AAACAACAAAAATAATAATCAA
1 AAACAACAAAAATAATAAGC-A
*
205620 AACAGCAACAAAAATAA-CAGCA
1 AA-A-CAACAAAAATAATAAGCA
* * *
205642 AAACAATAAAAACAAT-AGTAA
1 AAACAACAAAAATAATAAG-CA
205663 AAACAACAAAAATAAT-AGCA
1 AAACAACAAAAATAATAAGCA
205683 AAACA
1 AAACA
205688 GTACCAAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
20 18 0.32
21 18 0.32
22 5 0.09
23 3 0.05
24 12 0.21
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.10
Consensus pattern (21 bp):
AAACAACAAAAATAATAAGCA
Found at i:205690 original size:29 final size:27
Alignment explanation
Indices: 205658--205723 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
205648 TAAAAACAAT
205658 AGTAAAAACAACAAAAATAATAGCAAAAC
1 AGTAAAAAC-ACAAAAA-AATAGCAAAAC
* *
205687 AGTACCAAAACAGAAAAAAATATCAAAAC
1 AGTA--AAAACACAAAAAAATAGCAAAAC
*
205716 AGCAAAAA
1 AGTAAAAA
205724 ATTAGCATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 4 0.12
29 17 0.53
30 6 0.19
31 5 0.16
ACGTcount: A:0.68, C:0.15, G:0.08, T:0.09
Consensus pattern (27 bp):
AGTAAAAACACAAAAAAATAGCAAAAC
Found at i:205905 original size:24 final size:24
Alignment explanation
Indices: 205865--205912 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
205855 TGTCCAAATC
*
205865 CATTTTTCGGATCTATATTTTTGT
1 CATTTTTCAGATCTATATTTTTGT
205889 CATTTTTCAGA-CTTATATTTTTGT
1 CATTTTTCAGATC-TATATTTTTGT
205913 TCAAACTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.58
Consensus pattern (24 bp):
CATTTTTCAGATCTATATTTTTGT
Found at i:208508 original size:18 final size:19
Alignment explanation
Indices: 208485--208521 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
208475 TTTTAAAAAA
208485 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
208503 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
208522 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:208520 original size:19 final size:20
Alignment explanation
Indices: 208490--208561 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
208480 AAAAATATAA
208490 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
*
208510 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTATAAATT
*
208529 ATTTTAAATTTTT-TAAAATT
1 ATTTTGAATTTTTAT-AAATT
*
208549 ATTTTGTATTTTT
1 ATTTTGAATTTTT
208562 TGTTGAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.18
19 11 0.25
20 25 0.57
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:208546 original size:20 final size:19
Alignment explanation
Indices: 208497--208553 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
208487 TAAATTTTGG
*
208497 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTA
*
208516 AATTTTAAAAATTATTTTA
1 AATTTTTAAAATTATTTTA
208535 AATTTTTTAAAATTATTTT
1 AA-TTTTTAAAATTATTTT
208554 GTATTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.09
19 15 0.45
20 15 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTA
Found at i:208547 original size:10 final size:11
Alignment explanation
Indices: 208517--208553 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
208507 AATATTTTGA
208517 ATTTTAAAAATT
1 ATTTT-AAAATT
208529 ATTTT-AAATT
1 ATTTTAAAATT
208539 -TTTTAAAATT
1 ATTTTAAAATT
208549 ATTTT
1 ATTTT
208554 GTATTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.17
10 10 0.43
11 4 0.17
12 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:209045 original size:25 final size:24
Alignment explanation
Indices: 208997--209069 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 24
208987 TTTAACATTC
*
208997 TTTATATATTTTAAAAAAATATATAAT
1 TTTATA-ATTTT-TAAAAATATA-AAT
209024 TATTATAATTTCTTAAAAATATAAAT
1 T-TTATAATTT-TTAAAAATATAAAT
*
209050 TTTATAATTTTTATAAATAT
1 TTTATAATTTTTAAAAATAT
209070 TTTGAATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.21
25 9 0.21
26 4 0.10
27 14 0.33
28 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTATAATTTTTAAAAATATAAAT
Found at i:209092 original size:19 final size:19
Alignment explanation
Indices: 209043--209080 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
209033 TTCTTAAAAA
209043 TATAAAT-TTTAT-AATTTT
1 TATAAATATTT-TGAATTTT
209061 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
209080 T
1 T
209081 TTATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:209239 original size:53 final size:53
Alignment explanation
Indices: 209179--209285 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
209169 TGTAAAATTC
*
209179 AACTCGGTTCAAACTCGAAACTTGAATTACTTATTTGAGTTGAATCGAGATTT
1 AACTCGGTTCAAACTCGAAACTTGAATTACTTATTCGAGTTGAATCGAGATTT
209232 AACTCGGTTCAAACTCGAAACTTGAATTACTTATTCGAGTTGAATCGAGATTT
1 AACTCGGTTCAAACTCGAAACTTGAATTACTTATTCGAGTTGAATCGAGATTT
209285 A
1 A
209286 CTCACCTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (53 bp):
AACTCGGTTCAAACTCGAAACTTGAATTACTTATTCGAGTTGAATCGAGATTT
Found at i:211689 original size:27 final size:27
Alignment explanation
Indices: 211651--211703 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
211641 ACTATAATAG
211651 CTCGATTTTCAGTGGGGTCGAAAACAA
1 CTCGATTTTCAGTGGGGTCGAAAACAA
*
211678 CTCGATTTTCAGTGGTGTCGAAAACA
1 CTCGATTTTCAGTGGGGTCGAAAACA
211704 GTGGTTTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (27 bp):
CTCGATTTTCAGTGGGGTCGAAAACAA
Found at i:218671 original size:18 final size:19
Alignment explanation
Indices: 218643--218712 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 19
218633 GAAAATTAAT
218643 TAAATTAATTATGAAAGTC
1 TAAATTAATTATGAAAGTC
** *
218662 TAAA-TAATTACAAAATTGCC
1 TAAATTAATTATGAAA--GTC
218682 ATTAAATTAATTATGAAAGTC
1 --TAAATTAATTATGAAAGTC
218703 TAAA-TAATTA
1 TAAATTAATTA
218713 AATTAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
18 15 0.38
19 8 0.20
20 2 0.05
21 2 0.05
22 4 0.10
23 9 0.22
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (19 bp):
TAAATTAATTATGAAAGTC
Found at i:221841 original size:30 final size:30
Alignment explanation
Indices: 221789--222170 Score: 304
Period size: 29 Copynumber: 12.9 Consensus size: 30
221779 TTTGACTCCC
* ** *
221789 AAACTTCTCCAAAATTGTATTTTGACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
221819 AAACTTTTCCAAATTTTCATTTT-AGCCTCT
1 AAACTTTTCCAAAATTACATTTTAACCCT-T
* *
221849 AAACTTTT-TAAAATTATATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
221878 AAACGTTTT--AAAATTACATTTTAACCCTT
1 AAAC-TTTTCCAAAATTACATTTTAACCCTT
* * * *
221907 -AAC-TTTCTTAAAATCACATTTTGA-TCTT
1 AAACTTTTC-CAAAATTACATTTTAACCCTT
* *
221935 AAACTTTTTCAAAATTACATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
221965 AAACTTTTCCAAAATCACTTTTTGACCC-T
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* *
221994 AAAC-TTTCTAAAATCACATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
222023 AAACTTTTCTAAAATCACATTTTGACCC-T
1 AAACTTTTCCAAAATTACATTTTAACCCTT
*
222052 AAAC-TTTCCTAAAACTACATTTTAA-CCTT
1 AAACTTTTCC-AAAATTACATTTTAACCCTT
* * * *
222081 GAACTTTCCCAAAATCACATTTTTAACTCC-C
1 AAACTTTTCCAAAATTACA-TTTTAAC-CCTT
* * *
222112 AAACTTTTCGAAATTTTCATTTTAACCCTTT
1 AAACTTTTCCAAAATTACATTTTAACCC-TT
* * *
222143 AAACTTTTCTAAAATTCCATTTTGACCC
1 AAACTTTTCCAAAATTACATTTTAACCC
222171 ACACTTTATC
Statistics
Matches: 285, Mismatches: 48, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
26 3 0.01
28 32 0.11
29 107 0.38
30 104 0.36
31 37 0.13
32 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.41
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTAACCCTT
Found at i:221928 original size:58 final size:56
Alignment explanation
Indices: 221807--222235 Score: 302
Period size: 58 Copynumber: 7.3 Consensus size: 56
221797 CCAAAATTGT
* * * * * *
221807 ATTTTGACCCTTAAACTTTTCCAAATTTTCATTTTAGCCTCTAAACTTTTTAAAATTAT
1 ATTTTGACCCTTAAACTTTT--AAAATTACATTTTAACC-CTTAACTTTTTAAAATCAC
*
221866 ATTTTAACCCTTAAACGTTTTAAAATTACATTTTAACCCTTAACTTTCTTAAAATCAC
1 ATTTTGACCCTTAAAC-TTTTAAAATTACATTTTAACCCTTAACTTT-TTAAAATCAC
* * *
221924 ATTTTGA-TCTTAAACTTTTTCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCAC
1 ATTTTGACCCTTAAAC-TTTT-AAAATTACATTTTAA-CCCTTAACTTTT-TAAAATCAC
* *
221983 TTTTTGACCC-TAAACTTTCTAAAATCACATTTTAACCCTTAAACTTTTCTAAAATCAC
1 ATTTTGACCCTTAAACTTT-TAAAATTACATTTTAACCCTT-AACTTTT-TAAAATCAC
* **
222041 ATTTTGACCC-TAAACTTTCCTAAAACTACATTTTAA-CCTTGAACTTTCCCAAAATCAC
1 ATTTTGACCCTTAAACTTT--TAAAATTACATTTTAACCCTT-AACTTT-TTAAAATCAC
* * * *
222099 ATTTTTAACTCC-CAAACTTTTCGAAATTTTCATTTTAACCCTTTAAACTTTTCTAAAATTC-C
1 A-TTTTGAC-CCTTAAACTTTT--AAAATTACATTTTAACCC-TT-AACTTTT-TAAAA-TCAC
* * * * * *
222161 ATTTTGACCC--ACACTTTATCAAAATCACATTTTGA-CCTCGAACTTTCCTAAAACCAC
1 ATTTTGACCCTTAAACTTT-T-AAAATTACATTTTAACCCT-TAACTTT-TTAAAATCAC
*
222218 ATTTTGA-CCTTACACTTT
1 ATTTTGACCCTTAAACTTT
222236 CCCAAAATCA
Statistics
Matches: 305, Mismatches: 41, Indels: 49
0.77 0.10 0.12
Matches are distributed among these distances:
56 3 0.01
57 43 0.14
58 123 0.40
59 83 0.27
60 29 0.10
61 8 0.03
62 14 0.05
63 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.41
Consensus pattern (56 bp):
ATTTTGACCCTTAAACTTTTAAAATTACATTTTAACCCTTAACTTTTTAAAATCAC
Found at i:222218 original size:29 final size:29
Alignment explanation
Indices: 221907--222262 Score: 217
Period size: 29 Copynumber: 12.1 Consensus size: 29
221897 TTTAACCCTT
* * *
221907 AACTTTCTTAAAATCACATTTTGATCTTA
1 AACTTTCCTAAAATCACATTTTGACCTCA
* * * *
221936 AACTTT-TTCAAAATTACATTTTAACCCCTA
1 AACTTTCCT-AAAATCACATTTTGACCTC-A
*
221966 AACTTTTCC-AAAATCACTTTTTGACC-CTA
1 AAC-TTTCCTAAAATCACATTTTGACCTC-A
* *
221995 AACTTT-CTAAAATCACATTTTAACCCTTA
1 AACTTTCCTAAAATCACATTTTGA-CCTCA
*
222024 AACTTTTCTAAAATCACATTTTGACC-CTA
1 AACTTTCCTAAAATCACATTTTGACCTC-A
* **
222053 AACTTTCCTAAAA-CTACATTTTAACCTTG
1 AACTTTCCTAAAATC-ACATTTTGACCTCA
* * *
222082 AACTTTCCCAAAATCACATTTTTAACTCCCA
1 AACTTTCCTAAAATCACA-TTTTGAC-CTCA
* * * ** * *
222113 AACTTTTCGAAATTTTCATTTTAACCCTTTA
1 AACTTTCCTAAAATCACATTTTGA-CC-TCA
*
222144 AACTTTTCTAAAATTC-CATTTTGACC-CA
1 AACTTTCCTAAAA-TCACATTTTGACCTCA
* * *
222172 CACTTT-ATCAAAATCACATTTTGACCTCG
1 AACTTTCCT-AAAATCACATTTTGACCTCA
* *
222201 AACTTTCCTAAAACCACATTTTGACCTTA
1 AACTTTCCTAAAATCACATTTTGACCTCA
* * * * *
222230 CACTTTCCCAAAATCATATTTTTACCCCA
1 AACTTTCCTAAAATCACATTTTGACCTCA
222259 AACT
1 AACT
222263 CTTTGAAACT
Statistics
Matches: 256, Mismatches: 50, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.02
28 39 0.15
29 123 0.48
30 52 0.20
31 37 0.14
32 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTTCCTAAAATCACATTTTGACCTCA
Found at i:228630 original size:49 final size:50
Alignment explanation
Indices: 228411--228951 Score: 380
Period size: 50 Copynumber: 10.9 Consensus size: 50
228401 GAGAAAACAT
* * * ** * *
228411 GAAGATTTGAAGAGAAAGGTTAAGGCCATAATGGCGAACCTGGTACC-TCA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-A
* * * * *
228461 GAAGATGTGATGGGAAAGATTGAGGCCGCAACGGCAAATCCAGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * * *
228510 GAA-ATGTGATGGGAAAAGTTGAGGCCGCAACGGCGAACCTGATAGCATA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * *
228559 GAAGATGTGATGGGAAAGGTTGAGGCCGCAATGGCAAACCCGGTACCATA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * * * **
228609 -AAGATTTGAAGGGAAAAGTTGAGGTCGCAATGGTGAACCCAATACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * ** **
228657 GAAGATTTGAAGGGAAAGGTTGAGGCCGTAATGGCGAACCCGACACTTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * * ** ** *
228707 TAAGATATGATGGGAAAGGTTGAGGCCTCAACAACGAACTTGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * *
228757 GAAGATGTGATA-GGAAATGTTGAGGCCGCAACAGCTAACTCGGTACCATA
1 GAAGATGTGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * ** * * **
228807 -AAGATATGAAAGGAAAGGTTGAGGCCGCAACGGTAAACTCGATACTTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * * * * * *
228856 AAAGATGTGATGGG-AAGGATTGAGGTCGCAAAGACGAATCTGGCACCAT-
1 GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCATA
* * * * *
228905 GAAGATATGAAGCGAAAGGTTGAGGCCGCAATGACGAACCCAGTACC
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
228952 TTAAGAAAAC
Statistics
Matches: 384, Mismatches: 97, Indels: 21
0.76 0.19 0.04
Matches are distributed among these distances:
48 38 0.10
49 161 0.42
50 184 0.48
51 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.19
Consensus pattern (50 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATA
Found at i:228861 original size:99 final size:99
Alignment explanation
Indices: 228412--228935 Score: 391
Period size: 99 Copynumber: 5.3 Consensus size: 99
228402 AGAAAACATG
* * * ** * * *
228412 AAGATTTGAAGAGAAAGGTTAAGGCCATAATGGCGAAC-CTGGTACC-TCAGAAGATGTGATGGG
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTC-GATACCAT-AGAAGATGTGATAGG
* * * *
228475 AAAGATTGAGGCCGCAACGGC-AAATCCAGTACCATG
64 AAAGGTTGAGGCCGCAACGGCGAACT-CGGTACCATA
* * * * *
228511 AA-ATGTGATGGGAAAAGTTGAGGCCGCAACGGCGAAC-CTGATAGCATAGAAGATGTGATGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTC-GATACCATAGAAGATGTGATAGGA
* * *
228574 AAGGTTGAGGCCGCAATGGCAAACCCGGTACCATA
65 AAGGTTGAGGCCGCAACGGCGAACTCGGTACCATA
* * * * * * * *
228609 AAGATTTGAAGGGAAAAGTTGAGGTCGCAATGGTGAACCCAATACCAT-GAAGATTTGA-AGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAGAAGATGTGATA-GGA
* * * ** **
228672 AAGGTTGAGGCCGTAATGGCGAACCCGACACTTTA
65 AAGGTTGAGGCCGCAACGGCGAACTCGGTACCATA
* * ** * * *
228707 TAAGATATGATGGGAAAGGTTGAGGCCTCAACAACGAACTTGGTACCTTAGAAGATGTGATAGGA
1 -AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAGAAGATGTGATAGGA
* * *
228772 AATGTTGAGGCCGCAACAGCTAACTCGGTACCATA
65 AAGGTTGAGGCCGCAACGGCGAACTCGGTACCATA
* ** ** * *
228807 AAGATATGAAAGGAAAGGTTGAGGCCGCAACGGTAAACTCGATACTTTAAAAGATGTGAT-GGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAGAAGATGTGATAGGAA
* * * * *
228871 AGGATTGAGGTCGCAAAGACGAA-TCTGGCACCATG
66 AGG-TTGAGGCCGCAACGGCGAACTC-GGTACCATA
*
228906 AAGATATGAAGCGAAAGGTTGAGGCCGCAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAA
228936 TGACGAACCC
Statistics
Matches: 337, Mismatches: 78, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
98 125 0.37
99 173 0.51
100 38 0.11
101 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (99 bp):
AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAGAAGATGTGATAGGAA
AGGTTGAGGCCGCAACGGCGAACTCGGTACCATA
Found at i:228912 original size:198 final size:197
Alignment explanation
Indices: 228462--228944 Score: 504
Period size: 198 Copynumber: 2.4 Consensus size: 197
228452 GGTACCTCAG
* * * * * *
228462 AAGATGTGATGGGAAAGATTGAGGCCGCAACGGCAAATCCAGTACCATGAA-ATGTGATGGGAAA
1 AAGATGTGATGGGAAGGATTGAGGCCGCAAAGGCGAATCCGGCACCATGAAGATATGATGGGAAA
* ** * * *
228526 AGTTGAGGCCGCAACGGCGAACCTGATAGCATAGAAGATGTGATGGGAAAGGTTGAGGCCGCAAT
66 GGTTGAGGCCGCAACAACGAACCTGATACCATAGAAGATGTGATAGGAAAGGTTGAGGCCGCAAC
* * * * * *
228591 GGCAAACCCGGTACCATAAAGATTTGAAGGGAAAAGTTGAGGTCGCAATGGTGAACCCAATACCA
131 AGCAAACCCGGTACCATAAAGATATGAAAGGAAAAGTTGAGGCCGCAACGGTAAACCCAATACCA
*
228656 TG
196 TA
* * * * * * *
228658 AAGATTTGAAGGGAAAGG-TTGAGGCCGTAATGGCGAACCCGACACTTTAT-AAGATATGATGGG
1 AAGATGTGATGGG-AAGGATTGAGGCCGCAAAGGCGAATCCGGCAC--CATGAAGATATGATGGG
* * * * *
228721 AAAGGTTGAGGCCTCAACAACGAACTTGGTACCTTAGAAGATGTGATAGGAAATGTTGAGGCCGC
63 AAAGGTTGAGGCCGCAACAACGAACCTGATACCATAGAAGATGTGATAGGAAAGGTTGAGGCCGC
* * * * *
228786 AACAGCTAACTCGGTACCATAAAGATATGAAAGGAAAGGTTGAGGCCGCAACGGTAAACTCGATA
128 AACAGCAAACCCGGTACCATAAAGATATGAAAGGAAAAGTTGAGGCCGCAACGGTAAACCCAATA
**
228851 CTTTAA
193 CCAT-A
* * * * *
228857 AAGATGTGATGGGAAGGATTGAGGTCGCAAAGACGAATCTGGCACCATGAAGATATGAAGCGAAA
1 AAGATGTGATGGGAAGGATTGAGGCCGCAAAGGCGAATCCGGCACCATGAAGATATGATGGGAAA
**
228922 GGTTGAGGCCGCAATGACGAACC
66 GGTTGAGGCCGCAACAACGAACC
228945 CAGTACCTTA
Statistics
Matches: 227, Mismatches: 53, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
196 31 0.14
197 7 0.03
198 158 0.70
199 31 0.14
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (197 bp):
AAGATGTGATGGGAAGGATTGAGGCCGCAAAGGCGAATCCGGCACCATGAAGATATGATGGGAAA
GGTTGAGGCCGCAACAACGAACCTGATACCATAGAAGATGTGATAGGAAAGGTTGAGGCCGCAAC
AGCAAACCCGGTACCATAAAGATATGAAAGGAAAAGTTGAGGCCGCAACGGTAAACCCAATACCA
TA
Found at i:229025 original size:39 final size:39
Alignment explanation
Indices: 228972--229075 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 39
228962 ATGACGGGAA
* * *
228972 AGATTAAAG-CATCCAATTTCTTACCGAGATCATGGGGC
1 AGATTACAGTCATCCAATCTCTTACCCAGATCATGGGGC
* *
229010 AGATTACAGTCATCCAATCTCTTACCCCGATTATGGGGC
1 AGATTACAGTCATCCAATCTCTTACCCAGATCATGGGGC
* *
229049 AGATTGCAGTCATCCAATCTCATACCC
1 AGATTACAGTCATCCAATCTCTTACCC
229076 TTAAGTTAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 8 0.14
39 50 0.86
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (39 bp):
AGATTACAGTCATCCAATCTCTTACCCAGATCATGGGGC
Found at i:229115 original size:46 final size:45
Alignment explanation
Indices: 229058--229368 Score: 327
Period size: 46 Copynumber: 6.7 Consensus size: 45
229048 CAGATTGCAG
* * * *
229058 TCATCCAATCTCATACCCTTAAGTTAAGAAGGGTAGATTAAAGTCA
1 TCATCCAATCTCATACCCTTAAGTCAAG-AGGGCAGATTGAAGCCA
* * *
229104 TCATCCAATCTCATACCCCTGAGTCAAGAGAGGCAGATCGAAGCCA
1 TCATCCAATCTCATACCCTTAAGTCAAGAG-GGCAGATTGAAGCCA
*
229150 TCATCCAATCTCATACCCTTAAGTCAAGAAGGGCAGATTGAAGTCA
1 TCATCCAATCTCATACCCTTAAGTCAAG-AGGGCAGATTGAAGCCA
**
229196 TCATCTGATCTCATACCCTTAAGTCAAGAGGGGCAGATTGAAGCCA
1 TCATCCAATCTCATACCCTTAAGTCAAGA-GGGCAGATTGAAGCCA
* * * * *
229242 TCATCCAATCTCAAACCCCTAAAAGTCAAGAGACGTAGATTAAAGCCA
1 TCATCCAATCTCATA-CCCT-TAAGTCAAGAG-GGCAGATTGAAGCCA
*
229290 TCATCCAAATCTCATATCCC-TAAGTCAAGAGGGACAGATTGAAGTCA
1 TCATCC-AATCTCATA-CCCTTAAGTCAAGAGGG-CAGATTGAAGCCA
* * * * *
229337 TCATTCGATTTCATACCCCTTAGGTCATGAGG
1 TCATCCAATCTCATA-CCCTTAAGTCAAGAGG
229369 CAAAATAAAG
Statistics
Matches: 222, Mismatches: 34, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
45 3 0.01
46 139 0.63
47 42 0.19
48 27 0.12
49 11 0.05
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (45 bp):
TCATCCAATCTCATACCCTTAAGTCAAGAGGGCAGATTGAAGCCA
Found at i:229200 original size:92 final size:92
Alignment explanation
Indices: 229058--229363 Score: 375
Period size: 92 Copynumber: 3.3 Consensus size: 92
229048 CAGATTGCAG
*
229058 TCATCCAATCTCATA-CCCTTAAGTTAAGAAGGGTAGATTAAAGTCATCATCCAATCTCATACCC
1 TCATCCAATCTCATACCCCTTAAGTCAAGAAGGGTAGATTAAAGTCATCATCCAATCTCATACCC
* *
229122 CTGAGTCAAGAGAGGCAGATCGAAGCCA
66 CTAAGTCAAGAG-GGCAGATTGAAGCCA
* * **
229150 TCATCCAATCTCATA-CCCTTAAGTCAAGAAGGGCAGATTGAAGTCATCATCTGATCTCATACCC
1 TCATCCAATCTCATACCCCTTAAGTCAAGAAGGGTAGATTAAAGTCATCATCCAATCTCATACCC
*
229214 TTAAGTCAAGAGGGGCAGATTGAAGCCA
66 CTAAGTCAAGA-GGGCAGATTGAAGCCA
* * * *
229242 TCATCCAATCTCAAACCCCTAAAAGTCAAG-AGACGTAGATTAAAGCCATCATCCAAATCTCATA
1 TCATCCAATCTCATACCCCT-TAAGTCAAGAAG-GGTAGATTAAAGTCATCATCC-AATCTCATA
* *
229306 TCCCTAAGTCAAGAGGGACAGATTGAAGTCA
63 CCCCTAAGTCAAGAGGG-CAGATTGAAGCCA
* * * *
229337 TCATTCGATTTCATACCCCTTAGGTCA
1 TCATCCAATCTCATACCCCTTAAGTCA
229364 TGAGGCAAAA
Statistics
Matches: 183, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
92 96 0.52
93 7 0.04
94 32 0.17
95 48 0.26
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (92 bp):
TCATCCAATCTCATACCCCTTAAGTCAAGAAGGGTAGATTAAAGTCATCATCCAATCTCATACCC
CTAAGTCAAGAGGGCAGATTGAAGCCA
Found at i:229260 original size:138 final size:139
Alignment explanation
Indices: 229045--229368 Score: 401
Period size: 138 Copynumber: 2.3 Consensus size: 139
229035 CCCGATTATG
* * * * * *
229045 GGGCAGATTGCAGTCATC--C-AATCTCATACCCTTAAGTTAAGAAGGGTAGATTAAAGTCATCA
1 GGGCAGATTGAAGTCATCATCTGATCTCATACCCTTAAGTCAAGAGGGGCAGATTAAAGCCATCA
* * * *
229107 TCCAATCTCATACCCCT-GAGTCAAGAGAGGCAGATCGAAGCCATCATCC-AATCTCATA-CCCT
66 TCCAATCTCAAACCCCTAAAGTCAAGAGACGCAGATCAAAGCCATCATCCAAATCTCATATCCC-
229169 TAAGTCAAGAA
130 TAAGTCAAG-A
*
229180 GGGCAGATTGAAGTCATCATCTGATCTCATACCCTTAAGTCAAGAGGGGCAGATTGAAGCCATCA
1 GGGCAGATTGAAGTCATCATCTGATCTCATACCCTTAAGTCAAGAGGGGCAGATTAAAGCCATCA
* *
229245 TCCAATCTCAAACCCCTAAAAGTCAAGAGACGTAGATTAAAGCCATCATCCAAATCTCATATCCC
66 TCCAATCTCAAACCCCT-AAAGTCAAGAGACGCAGATCAAAGCCATCATCCAAATCTCATATCCC
229310 TAAGTCAAGA
130 TAAGTCAAGA
* * *
229320 GGGACAGATTGAAGTCATCAT-TCGATTTCATACCCCTTAGGTCATGAGG
1 GGG-CAGATTGAAGTCATCATCT-GATCTCATA-CCCTTAAGTCAAGAGG
229369 CAAAATAAAG
Statistics
Matches: 163, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
135 17 0.10
137 1 0.01
138 53 0.33
140 32 0.20
141 43 0.26
142 17 0.10
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (139 bp):
GGGCAGATTGAAGTCATCATCTGATCTCATACCCTTAAGTCAAGAGGGGCAGATTAAAGCCATCA
TCCAATCTCAAACCCCTAAAGTCAAGAGACGCAGATCAAAGCCATCATCCAAATCTCATATCCCT
AAGTCAAGA
Found at i:229781 original size:206 final size:207
Alignment explanation
Indices: 229424--229799 Score: 596
Period size: 206 Copynumber: 1.8 Consensus size: 207
229414 CTTCAAACCT
*
229424 CATCTTCTTGATGAGATACTGAGAAGTTGGCCAAAGCAATAAAGCGATCGTCTTCTTGATGAGAT
1 CATCTTCTTGATGAGATACTGAGAAGTGGGCCAAAGCAATAAAGCGA--GTCTTCTTGATGAGAT
*
229489 ACAAAGAAGTAGACCAAATTCATCTTCCTGATAAGATACAGAGAAGCGGATTAAAACAAGTGATG
64 ACAAAGAAGTAGACCAAATTCATCTTCCTAATAAGATACAGAGAAGCGGATTAAAACAAGTGATG
* *
229554 CGGTCATCTTCCTGATGAGATAC-AGAGAAGTAGACCAAATCGATGAAGCGAAGCTTAATGTGGT
129 AGGTCATCTTCCTGATGAGATACAAAAG-AGTAGACCAAATCGATGAAGCGAAGCTTAATGTGGT
229618 GAAACTTTGAACCCC
193 GAAACTTTGAACCCC
*
229633 CATCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCG-GTCTTCTTGATGAGATAC
1 CATCTTCTTGATGAGATACTGAGAAGTGGGCCAAAGCAATAAAGCGAGTCTTCTTGATGAGATAC
* * * *
229697 AAAGAAGTGGATCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTGA-GAA
66 AAAGAAGTAGACCAAATTCATCTTCCTAATAAGATACAGAGAAGCGGATTAAAACAAGTGATG-A
* *
229761 GGTTATCTTCTTGATGAGATACAAAAGAGTAGACCAAAT
130 GGTCATCTTCCTGATGAGATACAAAAGAGTAGACCAAAT
229800 TCATCTTCCT
Statistics
Matches: 154, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
205 1 0.01
206 106 0.69
207 3 0.02
209 44 0.29
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (207 bp):
CATCTTCTTGATGAGATACTGAGAAGTGGGCCAAAGCAATAAAGCGAGTCTTCTTGATGAGATAC
AAAGAAGTAGACCAAATTCATCTTCCTAATAAGATACAGAGAAGCGGATTAAAACAAGTGATGAG
GTCATCTTCCTGATGAGATACAAAAGAGTAGACCAAATCGATGAAGCGAAGCTTAATGTGGTGAA
ACTTTGAACCCC
Found at i:229785 original size:86 final size:85
Alignment explanation
Indices: 229633--229882 Score: 258
Period size: 86 Copynumber: 3.0 Consensus size: 85
229623 TTTGAACCCC
* * * * * * * *
229633 CATCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGG---TCTTCTTGATGAGAT
1 CATCTTCCTAATGAGATACAGAGAAGCGGATCAAAACAATGAAGAGGTCATCTTCTTGATGAGAT
* *
229695 ACAAAGAAGTGGATCAAATT
66 ACAAAGAAGTAGACCAAATT
* * *
229715 CGTCTTCCTAATGAGATACAGAGAAGCGGATTAAAACAAGTG-AGAAGGTTATCTTCTTGATGAG
1 CATCTTCCTAATGAGATACAGAGAAGCGGATCAAAACAA-TGAAG-AGGTCATCTTCTTGATGAG
229779 ATACAAA-AGAGTAGACCAAATT
64 ATACAAAGA-AGTAGACCAAATT
* * * * *
229801 CATCTTCCTAATGAGATACAGATAAGTGGATCGAAGCAATGAAGCGGTCATCTTCTTGATGAGAT
1 CATCTTCCTAATGAGATACAGAGAAGCGGATCAAAACAATGAAGAGGTCATCTTCTTGATGAGAT
* *
229866 ACAGAGAAGCAGACCAA
66 ACAAAGAAGTAGACCAA
229883 GAGATGAAGC
Statistics
Matches: 138, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
82 33 0.24
83 3 0.02
85 35 0.25
86 67 0.49
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (85 bp):
CATCTTCCTAATGAGATACAGAGAAGCGGATCAAAACAATGAAGAGGTCATCTTCTTGATGAGAT
ACAAAGAAGTAGACCAAATT
Found at i:231833 original size:30 final size:30
Alignment explanation
Indices: 231793--232250 Score: 369
Period size: 29 Copynumber: 15.5 Consensus size: 30
231783 CCAAAATTTT
* *
231793 ATTTTAACCCTCGAACTTTTCAAAAATCAC
1 ATTTTAACCCTCAAACTTTTCCAAAATCAC
* * * * * *
231823 ACTTTGACCCTTAAACTTCTCTAAAAT--T
1 ATTTTAACCCTCAAACTTTTCCAAAATCAC
* * * *
231851 ATATTGACCCTTAAACTTCTT-CAAAATTAC
1 ATTTTAACCCTCAAACTT-TTCCAAAATCAC
*
231881 ATTTTAA-CCTCAAACTTTTCCAAAATTAC
1 ATTTTAACCCTCAAACTTTTCCAAAATCAC
* *
231910 ATTTTGACCC-CTAAACTTTTCCAAAATCAT
1 ATTTTAACCCTC-AAACTTTTCCAAAATCAC
* *
231940 ATTTTAACCTTCAAATTTTTCCAAAATCAC
1 ATTTTAACCCTCAAACTTTTCCAAAATCAC
**
231970 ATTTTAACACC-CAAACTTTTTGAAAAAT-AC
1 ATTTTAAC-CCTCAAAC-TTTTCCAAAATCAC
* *
232000 ATTTTAACCCT-AAACTTTCCCAAAACCAC
1 ATTTTAACCCTCAAACTTTTCCAAAATCAC
232029 ATTTTAACCC-CAAAC-TTTCCTAAAATCAC
1 ATTTTAACCCTCAAACTTTTCC-AAAATCAC
* * *
232058 ATTTTTAACTCTCAAACTTTTCTAGAATCAC
1 A-TTTTAACCCTCAAACTTTTCCAAAATCAC
* *
232089 ATTTTAA-CCTCATAAACTTTTCTAAAATTAC
1 ATTTTAACCCTC--AAACTTTTCCAAAATCAC
* * *
232120 ATTTTGACCCTCACAC-TTTCTAAAAATCAC
1 ATTTTAACCCTCAAACTTTTC-CAAAATCAC
*
232150 ATTTTAA-CCTCAAAC-TTTCTTAAAA-CTAC
1 ATTTTAACCCTCAAACTTTTC-CAAAATC-AC
* *
232179 ATTTTAACCCT-AAAC-TTTCTTAAAACCAC
1 ATTTTAACCCTCAAACTTTTC-CAAAATCAC
* *
232208 ATTTTTACCC-CAAACTTTTCCAAAATTAC
1 ATTTTAACCCTCAAACTTTTCCAAAATCAC
232237 ATTTTAACCC-CAAA
1 ATTTTAACCCTCAAA
232251 TTCTTCGAAA
Statistics
Matches: 353, Mismatches: 50, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
28 35 0.10
29 136 0.39
30 128 0.36
31 46 0.13
32 8 0.02
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTTTAACCCTCAAACTTTTCCAAAATCAC
Found at i:231863 original size:28 final size:28
Alignment explanation
Indices: 231826--231942 Score: 108
Period size: 28 Copynumber: 4.1 Consensus size: 28
231816 AAATCACACT
*
231826 TTGACCCTTAAACTTCTCTAAAATTATA
1 TTGACCCTTAAACTTCTCCAAAATTATA
* *
231854 TTGACCCTTAAACTTCTTCAAAATTACA
1 TTGACCCTTAAACTTCTCCAAAATTATA
* * * * *
231882 TTTTAACCTCAAACTTTTCCAAAATTACATT
1 -TTGACCCTTAAACTTCTCCAAAATT--ATA
* * *
231913 TTGACCCCTAAACTTTTCCAAAATCATA
1 TTGACCCTTAAACTTCTCCAAAATTATA
231941 TT
1 TT
231943 TTAACCTTCA
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
28 29 0.41
29 20 0.29
30 20 0.29
31 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (28 bp):
TTGACCCTTAAACTTCTCCAAAATTATA
Found at i:231919 original size:59 final size:57
Alignment explanation
Indices: 231863--232250 Score: 361
Period size: 59 Copynumber: 6.5 Consensus size: 57
231853 ATTGACCCTT
* *
231863 AAACTTCTTCAAAATTACATTTTAACCTCAAACTTTTCCAAAATTACATTTTGACCCC
1 AAACTT-TTCAAAATTACATTTTAACCTCAAACTTTTCCAAAATCACATTTTAACCCC
* * *
231921 TAAACTTTTCCAAAATCATATTTTAACCTTCAAATTTTTCCAAAATCACATTTTAACACCC
1 -AAACTTTT-CAAAATTACATTTTAACC-TCAAACTTTTCCAAAATCACATTTTAAC-CCC
* * * *
231982 AAACTTTTTGAAAAATACATTTTAACC-CTAAACTTTCCCAAAACCACATTTTAACCCC
1 AAAC-TTTTCAAAATTACATTTTAACCTC-AAACTTTTCCAAAATCACATTTTAACCCC
* * * * *
232040 AAACTTTCCTAAAATCACATTTTTAACTCTCAAACTTTTCTAGAATCACATTTTAACCTCAT
1 AAACTTTTC-AAAATTACA-TTTTAAC-CTCAAACTTTTCCAAAATCACATTTTAACC-C-C
* * * *
232102 AAACTTTTCTAAAATTACATTTTGACCCTCACAC-TTTCTAAAAATCACATTTTAACCTC
1 AAACTTTTC-AAAATTACATTTT-AACCTCAAACTTTTC-CAAAATCACATTTTAACCCC
* * * * *
232161 AAACTTTCTTAAAACTACATTTTAACC-CTAAAC-TTTCTTAAAACCACATTTTTACCCC
1 AAACTTT-TCAAAATTACATTTTAACCTC-AAACTTTTC-CAAAATCACATTTTAACCCC
*
232219 AAACTTTTCCAAAATTACATTTTAACCCCAAA
1 AAACTTTT-CAAAATTACATTTTAACCTCAAA
232251 TTCTTCGAAA
Statistics
Matches: 273, Mismatches: 39, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
57 5 0.02
58 70 0.26
59 72 0.26
60 72 0.26
61 35 0.13
62 19 0.07
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (57 bp):
AAACTTTTCAAAATTACATTTTAACCTCAAACTTTTCCAAAATCACATTTTAACCCC
Found at i:232024 original size:119 final size:116
Alignment explanation
Indices: 231863--232250 Score: 396
Period size: 119 Copynumber: 3.3 Consensus size: 116
231853 ATTGACCCTT
* * * *
231863 AAACTTCTTCAAAATTACATTTTAA-CCTCAAACTTTTCCAAAATTACATTTTGACCCCTAAACT
1 AAACTTTTTCAAAATTACATTTTAACCCTCAAACTTTCCCAAAATCACATTTTAACCCC-AAAC-
*
231927 TTTCCAAAATCATATTTTAACCTTCAAATTTTTCCAAAATCACATTTTAACACCC
64 TTTCCAAAATCACATTTTAACCTTCAAATTTTT-CAAAATCACATTTTAAC-CCC
* * *
231982 AAACTTTTTGAAAAATACATTTTAACCCT-AAACTTTCCCAAAACCACATTTTAACCCCAAACTT
1 AAACTTTTTCAAAATTACATTTTAACCCTCAAACTTTCCCAAAATCACATTTTAACCCCAAACTT
* * *
232046 TCCTAAAATCACATTTTTAA-CTCTCAAACTTTTCTAGAATCACATTTTAACCTCAT
66 TCC-AAAATCACA-TTTTAACCT-TCAAATTTTTC-AAAATCACATTTTAACC-C-C
* * ** *
232102 AAAC-TTTTCTAAAATTACATTTTGACCCTCACACTTTCTAAAAATCACATTTTAACCTCAAACT
1 AAACTTTTTC-AAAATTACATTTTAACCCTCAAACTTTCCCAAAATCACATTTTAACCCCAAACT
* * * *
232166 TTCTTAAAA-CTACATTTTAACCCT-AAACTTTCTT-AAAACCACATTTTTACCCC
65 TTC-CAAAATC-ACATTTTAACCTTCAAA-TTT-TTCAAAATCACATTTTAACCCC
*
232219 AAACTTTTCCAAAATTACATTTTAACCC-CAAA
1 AAACTTTTTCAAAATTACATTTTAACCCTCAAA
232251 TTCTTCGAAA
Statistics
Matches: 225, Mismatches: 29, Indels: 33
0.78 0.10 0.11
Matches are distributed among these distances:
116 3 0.01
117 26 0.12
118 21 0.09
119 99 0.44
120 34 0.15
121 42 0.19
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (116 bp):
AAACTTTTTCAAAATTACATTTTAACCCTCAAACTTTCCCAAAATCACATTTTAACCCCAAACTT
TCCAAAATCACATTTTAACCTTCAAATTTTTCAAAATCACATTTTAACCCC
Found at i:232189 original size:179 final size:178
Alignment explanation
Indices: 231863--232250 Score: 493
Period size: 179 Copynumber: 2.2 Consensus size: 178
231853 ATTGACCCTT
* * *
231863 AAACTTCTT-CAAAATTACA-TTTTAACCTCAAACTTTTCCAAAATTACATTTTGACCCCTAAAC
1 AAACTT-TTCCAAAATTACATTTTTAACCTCAAACTTTTCCAAAATCACATTTTAACCCATAAAC
* * * *
231926 TTTTCCAAAATCATATTTTAACCTTCAAATTTTTCCAAAATCACATTTTAACACCCAAACTTTTT
65 TTTTCCAAAATCACATTTTAACCCTCAAATTTCTCAAAAATCACATTTTAACACCCAAACTTTTT
231991 GAAAAATACATTTTAACCCTAAACTTTCCCAAAACCACATTTTAACCCC
130 GAAAAATACATTTTAACCCTAAACTTTCCCAAAACCACATTTTAACCCC
* * *
232040 AAAC-TTTCCTAAAATCACATTTTTAACTCTCAAACTTTTCTAGAATCACATTTTAACCTCATAA
1 AAACTTTTCC-AAAATTACATTTTTAAC-CTCAAACTTTTCCAAAATCACATTTTAACC-CATAA
* * * * *
232104 ACTTTTCTAAAATTACATTTTGACCCTCACACTTTCT-AAAAATCACATTTTAAC-CTCAAACTT
63 ACTTTTCCAAAATCACATTTTAACCCTCA-AATTTCTCAAAAATCACATTTTAACACCCAAACTT
* ** *
232167 TCTT-AAAACTACATTTTAACCCTAAACTTTCTTAAAACCACATTTTTACCCC
127 T-TTGAAAAATACATTTTAACCCTAAACTTTCCCAAAACCACATTTTAACCCC
*
232219 AAACTTTTCCAAAATTACA-TTTTAACCCCAAA
1 AAACTTTTCCAAAATTACATTTTTAACCTCAAA
232251 TTCTTCGAAA
Statistics
Matches: 182, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
175 2 0.01
176 2 0.01
177 17 0.09
178 14 0.08
179 91 0.50
180 51 0.28
181 5 0.03
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (178 bp):
AAACTTTTCCAAAATTACATTTTTAACCTCAAACTTTTCCAAAATCACATTTTAACCCATAAACT
TTTCCAAAATCACATTTTAACCCTCAAATTTCTCAAAAATCACATTTTAACACCCAAACTTTTTG
AAAAATACATTTTAACCCTAAACTTTCCCAAAACCACATTTTAACCCC
Found at i:237929 original size:17 final size:18
Alignment explanation
Indices: 237896--237930 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
237886 AAGGTTAAAA
237896 TTAAAAATAAATAATCTT
1 TTAAAAATAAATAATCTT
*
237914 TTAAAAATTAAT-ATCTT
1 TTAAAAATAAATAATCTT
237931 CTTTTATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAAATAAATAATCTT
Found at i:241686 original size:24 final size:24
Alignment explanation
Indices: 241635--241686 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
241625 GCCCTCCTCA
* *
241635 TTCTCCTTTTACTAGAGGATAGTT
1 TTCTCCTTTTACTAGAGGATAATC
241659 TTCTCCTTTTACTAGAAGG-TAATC
1 TTCTCCTTTTACTAG-AGGATAATC
241683 TTCT
1 TTCT
241687 AAATTTGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.46
Consensus pattern (24 bp):
TTCTCCTTTTACTAGAGGATAATC
Found at i:246625 original size:15 final size:15
Alignment explanation
Indices: 246605--246636 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
246595 TATTTTGTTG
246605 GATTCAGAAAGAGTA
1 GATTCAGAAAGAGTA
*
246620 GATTCAGATAGAGTA
1 GATTCAGAAAGAGTA
246635 GA
1 GA
246637 AAGAGACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (15 bp):
GATTCAGAAAGAGTA
Found at i:257853 original size:22 final size:21
Alignment explanation
Indices: 257827--257875 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
257817 ATTTTGAGAA
* *
257827 AAAGAAAGAAAAGAAAAAGAG
1 AAAGAAAGAAAAAAAAAAAAG
*
257848 ACAAGAATGAAAAAAAAAAAAG
1 A-AAGAAAGAAAAAAAAAAAAG
257870 AAAGAA
1 AAAGAA
257876 TTTGTTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAAAAAG
Found at i:261999 original size:15 final size:15
Alignment explanation
Indices: 261979--262024 Score: 92
Period size: 15 Copynumber: 3.1 Consensus size: 15
261969 CGACAGTAAG
261979 GGGGAGAAAAAATTT
1 GGGGAGAAAAAATTT
261994 GGGGAGAAAAAATTT
1 GGGGAGAAAAAATTT
262009 GGGGAGAAAAAATTT
1 GGGGAGAAAAAATTT
262024 G
1 G
262025 AGTTTTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.20
Consensus pattern (15 bp):
GGGGAGAAAAAATTT
Found at i:263474 original size:26 final size:26
Alignment explanation
Indices: 263444--263494 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
263434 GAAATACCAT
263444 ATTTTATTATTATTATATAGATATAG
1 ATTTTATTATTATTATATAGATATAG
263470 ATTTTATTATTATTATATAGATATA
1 ATTTTATTATTATTATATAGATATA
263495 TCCAACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (26 bp):
ATTTTATTATTATTATATAGATATAG
Found at i:263487 original size:20 final size:22
Alignment explanation
Indices: 263450--263491 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
263440 CCATATTTTA
263450 TTATTATTATATAGATATAGATT
1 TTATTATTATATA-ATATAGATT
263473 TTATTATTAT-T-ATATAGAT
1 TTATTATTATATAATATAGAT
263492 ATATCCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TTATTATTATATAATATAGATT
Found at i:263511 original size:21 final size:21
Alignment explanation
Indices: 263485--263525 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
263475 ATTATTATTA
*
263485 TATAGATATATCCAACTTTTC
1 TATAGATATATACAACTTTTC
*
263506 TATAGATATATAGAACTTTT
1 TATAGATATATACAACTTTT
263526 ATCAGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
TATAGATATATACAACTTTTC
Done.