Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012425.1 Kokia drynarioides strain JFW-HI SEQ_127429, 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: 203836
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:588 original size:30 final size:29
Alignment explanation
Indices: 531--823 Score: 335
Period size: 30 Copynumber: 10.0 Consensus size: 29
521 CCCTGAAGGT
*
531 CCCAAAACTATCAAAAAATTCCATTTTTAC
1 CCCAAAACT-TCCAAAAATTCCATTTTTAC
** *
561 CCCCGAACTTCCAAAAATCCCATTTTTTAC
1 CCCAAAACTTCCAAAAATTCCA-TTTTTAC
*
591 CCCAAAACTTCCAACAATTCCA-TTTTA-
1 CCCAAAACTTCCAAAAATTCCATTTTTAC
* *
618 CCCATGAACTTACAAAAATTCCATTTTTGAC
1 CCCA-AAACTTCCAAAAATTCCATTTTT-AC
*
649 CCCAAAAGTTCCAAAAATTCCATTTTTAC
1 CCCAAAACTTCCAAAAATTCCATTTTTAC
*
678 CCTC-GAACTTCCAAAAATTCCATTTTTGAC
1 CC-CAAAACTTCCAAAAATTCCATTTTT-AC
*
708 CCCAAAACTTCTAAAAATTCCATTTTTAC
1 CCCAAAACTTCCAAAAATTCCATTTTTAC
* *
737 CCCCAAACTT-CAAAAAATCCTATTTTTTAC
1 CCCAAAACTTCCAAAAATTCC-A-TTTTTAC
* *
767 CCTAAAACTTTCAAAAATTCCATTTTTAGC
1 CCCAAAACTTCCAAAAATTCCATTTTTA-C
*
797 CCC-AAACTTCTAAAAATTCCATTTTTA
1 CCCAAAACTTCCAAAAATTCCATTTTTA
824 ACCTCGAATT
Statistics
Matches: 224, Mismatches: 27, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.02
28 28 0.12
29 81 0.36
30 98 0.44
31 13 0.06
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCAAAACTTCCAAAAATTCCATTTTTAC
Found at i:703 original size:59 final size:59
Alignment explanation
Indices: 531--822 Score: 390
Period size: 59 Copynumber: 4.9 Consensus size: 59
521 CCCTGAAGGT
* * *
531 CCCAAAACTATCAAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTAC
1 CCCAAAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAC
* ** *
591 CCCAAAACTTCCAACAATTCCA-TTTTACCCATGAACTTACAAAAATTCCATTTTTGAC
1 CCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAC
* *
649 CCCAAAAGTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGAC
1 CCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAC
* * * *
708 CCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTT-CAAAAAATCCTATTTTTTAC
1 CCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCC-ATTTTTGAC
* * * * *
767 CCTAAAACTTTCAAAAATTCCATTTTTAGCCCCAAACTTCTAAAAATTCCATTTTT
1 CCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT
823 AACCTCGAAT
Statistics
Matches: 205, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
58 60 0.29
59 128 0.62
60 17 0.08
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
CCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAC
Found at i:2881 original size:21 final size:21
Alignment explanation
Indices: 2855--2897 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2845 TCATCATCAC
*
2855 AAGAACACATCAAAAAGATTG
1 AAGAACAAATCAAAAAGATTG
* *
2876 AAGAACAAATCCAAAAGTTTG
1 AAGAACAAATCAAAAAGATTG
2897 A
1 A
2898 CAAGATTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (21 bp):
AAGAACAAATCAAAAAGATTG
Found at i:6478 original size:42 final size:41
Alignment explanation
Indices: 6431--6511 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 41
6421 AACTATGAGT
* *
6431 ATTAGTTCCTACCATAACTAATCCAACAACCCAAAGTCAAAC
1 ATTAGTTCCTAACATAACTAAACCAACAACCC-AAGTCAAAC
* * *
6473 ATTAGTTCCTAATATAATTAAACCAACTACCCAAGTCAA
1 ATTAGTTCCTAACATAACTAAACCAACAACCCAAGTCAA
6512 CGTCTTCAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 7 0.21
42 27 0.79
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (41 bp):
ATTAGTTCCTAACATAACTAAACCAACAACCCAAGTCAAAC
Found at i:20086 original size:266 final size:266
Alignment explanation
Indices: 19600--20139 Score: 1037
Period size: 266 Copynumber: 2.0 Consensus size: 266
19590 TTTTGTTTTC
19600 TTTTT-TTTTCATGTAGTAGGGAAAGCGGCAGTGGAGGTCAAGTAGGTATACAAAATGAATTGGC
1 TTTTTGTTTTCATGTAGTAGGGAAAGCGGCAGTGGAGGTCAAGTAGGTATACAAAATGAATTGGC
*
19664 AAATCTTACGTTGATTAATGAAGAGGGAGAAATCTTACTAGTTCAAAGCGAGGTTGATCCTGCCA
66 AAATCTTACGTTGAATAATGAAGAGGGAGAAATCTTACTAGTTCAAAGCGAGGTTGATCCTGCCA
19729 AGGAGGTTTATGATTTATGTTTGGTAAGATGTTTTCTCACGATAAGCGTTATTAATTTTCCAGCA
131 AGGAGGTTTATGATTTATGTTTGGTAAGATGTTTTCTCACGATAAGCGTTATTAATTTTCCAGCA
19794 ATGGAAAGCACTATGGCAAACTTGTGGCATCCTGTGAGAGGGTTTAGATCTTAAATCTGGGACAA
196 ATGGAAAGCACTATGGCAAACTTGTGGCATCCTGTGAGAGGGTTTAGATCTTAAATCTGGGACAA
19859 AAATGA
261 AAATGA
*
19865 TTTTTGTTTTCATGTAGTAGGGAAAGCGGCAGTGGAGGTCAAGTAGGTATAGAAAATGAATTGGC
1 TTTTTGTTTTCATGTAGTAGGGAAAGCGGCAGTGGAGGTCAAGTAGGTATACAAAATGAATTGGC
*
19930 AAATCTTACGTTGAATAATGAAGAGGGGGAAATCTTACTAGTTCAAAGCGAGGTTGATCCTGCCA
66 AAATCTTACGTTGAATAATGAAGAGGGAGAAATCTTACTAGTTCAAAGCGAGGTTGATCCTGCCA
19995 AGGAGGTTTATGATTTATGTTTGGTAAGATGTTTTCTCACGATAAGCGTTATTAATTTTCCAGCA
131 AGGAGGTTTATGATTTATGTTTGGTAAGATGTTTTCTCACGATAAGCGTTATTAATTTTCCAGCA
*
20060 ATGGAAAGCACTATGGCAACCTTGTGGCATCCTGTGAGAGGGTTTAGATCTTAAATCTGGGACAA
196 ATGGAAAGCACTATGGCAAACTTGTGGCATCCTGTGAGAGGGTTTAGATCTTAAATCTGGGACAA
20125 AAATGA
261 AAATGA
20131 TTTTTGTTT
1 TTTTTGTTT
20140 CGTTTCGTCC
Statistics
Matches: 270, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
265 5 0.02
266 265 0.98
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (266 bp):
TTTTTGTTTTCATGTAGTAGGGAAAGCGGCAGTGGAGGTCAAGTAGGTATACAAAATGAATTGGC
AAATCTTACGTTGAATAATGAAGAGGGAGAAATCTTACTAGTTCAAAGCGAGGTTGATCCTGCCA
AGGAGGTTTATGATTTATGTTTGGTAAGATGTTTTCTCACGATAAGCGTTATTAATTTTCCAGCA
ATGGAAAGCACTATGGCAAACTTGTGGCATCCTGTGAGAGGGTTTAGATCTTAAATCTGGGACAA
AAATGA
Found at i:22816 original size:44 final size:44
Alignment explanation
Indices: 22753--22838 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
22743 GCTTTATTAG
22753 TTATCAACAAATGCAACTCGAATACACAAGATAAATAAAAAATC
1 TTATCAACAAATGCAACTCGAATACACAAGATAAATAAAAAATC
22797 TTATCAACAAATGCAACTCGAATACACAAGATAAATAAAAAA
1 TTATCAACAAATGCAACTCGAATACACAAGATAAATAAAAAA
22839 ACGGAGCCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.20
Consensus pattern (44 bp):
TTATCAACAAATGCAACTCGAATACACAAGATAAATAAAAAATC
Found at i:29163 original size:17 final size:17
Alignment explanation
Indices: 29141--29209 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
29131 TTTATTGTCC
29141 TTTATTTTATTTTACTA
1 TTTATTTTATTTTACTA
*
29158 TTTATTATTTATTCATT-TTCA
1 TTTA-T-TTTATT--TTACT-A
*
29179 TTTATTTTATCTTACTA
1 TTTATTTTATTTTACTA
*
29196 TTTATTTTACTTTA
1 TTTATTTTATTTTA
29210 TTTTGCATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
17 19 0.46
18 2 0.05
19 11 0.27
20 2 0.05
21 7 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTTATTTTACTA
Found at i:29183 original size:38 final size:38
Alignment explanation
Indices: 29124--29201 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
29114 CTTTTTATAT
* * *
29124 TTATTTATTTATTGTCCTTTATTTTATTTTACTATTTA
1 TTATTTATTCATTGTCATTTATTTTATCTTACTATTTA
*
29162 TTATTTATTCATTTTCATTTATTTTATCTTACTATTTA
1 TTATTTATTCATTGTCATTTATTTTATCTTACTATTTA
29200 TT
1 TT
29202 TTACTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.09, G:0.01, T:0.68
Consensus pattern (38 bp):
TTATTTATTCATTGTCATTTATTTTATCTTACTATTTA
Found at i:29935 original size:13 final size:14
Alignment explanation
Indices: 29917--29945 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29907 AAGTTGAGAC
29917 TCGAAAAAAG-GTT
1 TCGAAAAAAGAGTT
29930 TCGAAAAAAGAGTT
1 TCGAAAAAAGAGTT
29944 TC
1 TC
29946 ATTCTCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (14 bp):
TCGAAAAAAGAGTT
Found at i:43311 original size:20 final size:19
Alignment explanation
Indices: 43270--43326 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
43260 AGCCCTCGTG
**
43270 GTATCGATATTTTTTATGA
1 GTATCGATATTTTTTAAAA
43289 GTATCGATATTTTTATAAAA
1 GTATCGATATTTTT-TAAAA
43309 GTATCGATATTTTTTAAA
1 GTATCGATATTTTTTAAA
43327 TGGCATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (19 bp):
GTATCGATATTTTTTAAAA
Found at i:51879 original size:24 final size:23
Alignment explanation
Indices: 51850--51913 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
51840 ATTTTATTCA
51850 TTATTTATTTTTTATTTGTTGCTT-
1 TTATTTATTTTTTATTTG--GCTTG
*
51874 TTATTT-TGTTCATTAATTTGGCTTG
1 TTATTTAT-TT--TTTATTTGGCTTG
51899 TTATTTATTTTTTAT
1 TTATTTATTTTTTAT
51914 GAAATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
23 5 0.15
24 12 0.36
25 8 0.24
26 8 0.24
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (23 bp):
TTATTTATTTTTTATTTGGCTTG
Found at i:52224 original size:22 final size:21
Alignment explanation
Indices: 52198--52245 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
52188 ATCCTTATCG
*
52198 TATTTTA-TTATGATTACTTTTT
1 TATTTTATTTATG-TTA-TTTGT
52220 TATTTTATTTATGTTATTTGT
1 TATTTTATTTATGTTATTTGT
52241 TATTT
1 TATTT
52246 ATCGTGTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (21 bp):
TATTTTATTTATGTTATTTGT
Found at i:53563 original size:3 final size:3
Alignment explanation
Indices: 53550--53581 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
53540 AAATGAGTCT
53550 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53582 CTTTCTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:56362 original size:22 final size:22
Alignment explanation
Indices: 56331--56381 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
56321 CATACAAGGG
*
56331 TGAGAAAAATAAGAAAAGGGTT
1 TGAGAGAAATAAGAAAAGGGTT
56353 TGAGAGAAATAAGAAAAGGGTT
1 TGAGAGAAATAAGAAAAGGGTT
56375 TGAGAGA
1 TGAGAGA
56382 TATCAAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (22 bp):
TGAGAGAAATAAGAAAAGGGTT
Found at i:65935 original size:102 final size:99
Alignment explanation
Indices: 65664--65937 Score: 268
Period size: 99 Copynumber: 2.7 Consensus size: 99
65654 TCTCCCCTGT
* * * *
65664 AGTTGCAGTGGAATAGAGTGAAGT-CACATCCAAATCCTATATCCCTAAAGATGCAATGGATTGG
1 AGTTGCAGTGGAATGGAGTGAAGTCCACA-CCAAATCCTATAT-CCTGAAGTTGCAA-GGATCGG
* * *
65728 ATT-CAACTAATAGCACTAAATCTTAATCTCCACTAA
63 ATTAAAACTAATAGAACTAAATCTTAATATCCACTAA
* * ** *
65764 AGTTGTAGTGGAATGGAGTGAAG-CCACACCAAATCCTATATCCTTGAAGTTGCAAGGGTCAAAC
1 AGTTGCAGTGGAATGGAGTGAAGTCCACACCAAATCCTATATCC-TGAAGTTGCAAGGATCGGAT
* * * * * *
65828 CAAAACTAGTCGTAAC-ACATCTTAATATTCACTGA
65 TAAAACTAATAG-AACTAAATCTTAATATCCACTAA
* *
65863 AGTTGCAGTGAAATGGAGTGAAGTTCCAAACCCAAATCCTATATCTCTGAAGTTGCAAGGATCGG
1 AGTTGCAGTGGAATGGAGTGAAG-TCCACA-CCAAATCCTATATC-CTGAAGTTGCAAGGATCGG
65928 ATTAAAACTA
63 ATTAAAACTA
65938 CAATAGCAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
98 6 0.04
99 65 0.46
100 27 0.19
101 4 0.03
102 37 0.26
103 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (99 bp):
AGTTGCAGTGGAATGGAGTGAAGTCCACACCAAATCCTATATCCTGAAGTTGCAAGGATCGGATT
AAAACTAATAGAACTAAATCTTAATATCCACTAA
Found at i:67973 original size:3 final size:3
Alignment explanation
Indices: 67965--67989 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
67955 TGTATGCAAA
67965 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
67990 AATTGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:74000 original size:36 final size:39
Alignment explanation
Indices: 73941--74021 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 39
73931 CAATAAATTT
* * * *
73941 AAAAAATATATAATATATCAAATACATTTAAAACAT-TA
1 AAAAAATATAAAATAAATCAAATAAATTTAAAAAATATA
73979 AAAAAATA-AAAATAAAT-AAATAAATTTAAAAAATATA
1 AAAAAATATAAAATAAATCAAATAAATTTAAAAAATATA
74016 AAAAAA
1 AAAAAA
74022 AGTCTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 15 0.39
37 15 0.39
38 8 0.21
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (39 bp):
AAAAAATATAAAATAAATCAAATAAATTTAAAAAATATA
Found at i:74188 original size:24 final size:22
Alignment explanation
Indices: 74160--74239 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 22
74150 ATCCAACAAC
*
74160 AAAAATAACAACAAAAACAATA
1 AAAAAAAACAACAAAAACAATA
* * *
74182 ATAAAAATAACAGCCAAAACAACA
1 A-AAAAA-AACAACAAAAACAATA
* * *
74206 ACAAAAAAC-ACCAAAATAATA
1 AAAAAAAACAACAAAAACAATA
74227 AAAAAAAACAACA
1 AAAAAAAACAACA
74240 CCAAAACAGC
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 17 0.38
22 6 0.13
23 8 0.18
24 14 0.31
ACGTcount: A:0.74, C:0.17, G:0.01, T:0.07
Consensus pattern (22 bp):
AAAAAAAACAACAAAAACAATA
Found at i:74205 original size:45 final size:43
Alignment explanation
Indices: 74128--74255 Score: 125
Period size: 45 Copynumber: 2.9 Consensus size: 43
74118 AAACAATAGT
* *
74128 AAAAACACATAAAAAAAATAATATCC--AACAACAAAAATAACAAC
1 AAAAACA-ATAAAAAAAATAACA-CCAAAACAACAAAAAAAAC-AC
*
74172 AAAAACAATAATAAAAATAACAGCCAAAACAACAACAAAAAACAC
1 AAAAACAATAAAAAAAATAACA-CCAAAACAACAA-AAAAAACAC
* * * *
74217 CAAAATAATAAAAAAAAACAACACCAAAACAGCAAAAAA
1 AAAAACAAT-AAAAAAAATAACACCAAAACAACAAAAAA
74256 TAGTAACCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 15 0.21
44 11 0.15
45 28 0.39
46 17 0.24
ACGTcount: A:0.72, C:0.19, G:0.02, T:0.08
Consensus pattern (43 bp):
AAAAACAATAAAAAAAATAACACCAAAACAACAAAAAAAACAC
Found at i:74245 original size:12 final size:12
Alignment explanation
Indices: 74153--74212 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
74143 AAATAATATC
74153 CAACAACAAAAA
1 CAACAACAAAAA
*
74165 TAACAACAAAAA
1 CAACAACAAAAA
* *
74177 CAATAATAAAAA
1 CAACAACAAAAA
* * *
74189 TAACAGCCAAAA
1 CAACAACAAAAA
74201 CAACAACAAAAA
1 CAACAACAAAAA
74213 ACACCAAAAT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.72, C:0.20, G:0.02, T:0.07
Consensus pattern (12 bp):
CAACAACAAAAA
Found at i:74253 original size:21 final size:21
Alignment explanation
Indices: 74184--74288 Score: 70
Period size: 22 Copynumber: 4.8 Consensus size: 21
74174 AAACAATAAT
*
74184 AAAAATAACAGCCAAAACAACA
1 AAAAATAACA-CCAAAACAGCA
* **
74206 ACAAAA-AACACCAAAATAATAAAA
1 A-AAAATAACACC--AA-AACAGCA
*
74230 AAAAACAACACCAAAACAGCA
1 AAAAATAACACCAAAACAGCA
*
74251 AAAAATAGTA-ACCAAAACAGTA
1 AAAAATA--ACACCAAAACAGCA
*
74273 AAAAATAGCACCAAAA
1 AAAAATAACACCAAAA
74289 TAATAATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
21 19 0.28
22 25 0.37
23 11 0.16
24 12 0.18
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAATAACACCAAAACAGCA
Found at i:74253 original size:24 final size:23
Alignment explanation
Indices: 74154--74255 Score: 77
Period size: 24 Copynumber: 4.5 Consensus size: 23
74144 AATAATATCC
* *
74154 AACAACAAAAATAACAACA--AA
1 AACAACAAAAAAAAAAACACCAA
* * *
74175 AACAATAATAAAAATAACAGCCAA
1 AACAACAAAAAAAAAAACA-CCAA
*
74199 AACAAC--AACAAAAAACACCAA
1 AACAACAAAAAAAAAAACACCAA
* *
74220 AATAATAAAAAAAAACAACACCAA
1 AACAACAAAAAAAAA-AACACCAA
*
74244 AACAGCAAAAAA
1 AACAACAAAAAA
74256 TAGTAACCAA
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
21 23 0.38
22 8 0.13
23 6 0.10
24 24 0.39
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.06
Consensus pattern (23 bp):
AACAACAAAAAAAAAAACACCAA
Found at i:74278 original size:22 final size:21
Alignment explanation
Indices: 74239--74288 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
74229 AAAAAACAAC
74239 ACCAAAACAGCAAAAAATAGTA
1 ACCAAAACAGCAAAAAATAG-A
* *
74261 ACCAAAACAGTAAAAAATAGC
1 ACCAAAACAGCAAAAAATAGA
74282 ACCAAAA
1 ACCAAAA
74289 TAATAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (21 bp):
ACCAAAACAGCAAAAAATAGA
Found at i:76149 original size:26 final size:26
Alignment explanation
Indices: 76116--76172 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
76106 TGTTAAAGTG
76116 ATAAATTTACAATGAATTAAGGTGAA
1 ATAAATTTACAATGAATTAAGGTGAA
76142 ATAAATTTACAATGAATTAAGGTGAA
1 ATAAATTTACAATGAATTAAGGTGAA
76168 ATAAA
1 ATAAA
76173 ATGGTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.30
Consensus pattern (26 bp):
ATAAATTTACAATGAATTAAGGTGAA
Found at i:76321 original size:17 final size:18
Alignment explanation
Indices: 76288--76323 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
76278 ATTTTACTAT
76288 TGAAATTAATTAATTTAA
1 TGAAATTAATTAATTTAA
*
76306 TGAAATT-ATTATTTTAA
1 TGAAATTAATTAATTTAA
76323 T
1 T
76324 CAAGAATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TGAAATTAATTAATTTAA
Found at i:77072 original size:42 final size:42
Alignment explanation
Indices: 77000--77108 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
76990 AAATCACTTG
* * *
77000 ATGTATAAATGGAAGACCCATGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAA-GGAAGACTCATGTCTAGGGATGAGCATGAGATT
*
77043 ATGTTTAAAGGAAGACTCGTGTCTAGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTAGGGATGAGCATGAGATT
*
77085 ATGTTTAAAGGAAGACTTATGTCT
1 ATGTTTAAAGGAAGACTCATGTCT
77109 CAGTAAAGCA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 52 0.87
43 8 0.13
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTAGGGATGAGCATGAGATT
Found at i:80848 original size:21 final size:21
Alignment explanation
Indices: 80792--80838 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
80782 TTTTATTACT
*
80792 AGTGGTTTATCCAC-A--ATG
1 AGTGGTTTGTCCACAACGATG
80810 AGTGGTTTGTCCACAACGATG
1 AGTGGTTTGTCCACAACGATG
80831 AGTGGTTT
1 AGTGGTTT
80839 AGCCATAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 13 0.52
19 1 0.04
21 11 0.44
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (21 bp):
AGTGGTTTGTCCACAACGATG
Found at i:82531 original size:16 final size:16
Alignment explanation
Indices: 82497--82543 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
82487 AAATTTTCAA
*
82497 AAAATAA-AAAATGTAT
1 AAAATAATAAAATAT-T
* *
82513 AAAATTATTAAATATT
1 AAAATAATAAAATATT
82529 AAAATAATAAAATAT
1 AAAATAATAAAATAT
82544 AAATATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAATAATAAAATATT
Found at i:83673 original size:30 final size:29
Alignment explanation
Indices: 83639--83708 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 29
83629 TTATAATATT
83639 TTTATAAAAATTCTAATAAAT-TATTAAAAA
1 TTTATAAAAA-T-TAATAAATATATTAAAAA
*
83669 TTTAT-AAAATTAATAAATCATATTTAAAA
1 TTTATAAAAATTAATAAAT-ATATTAAAAA
83698 TTTATTAAAAA
1 TTTA-TAAAAA
83709 AATTATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 8 0.23
28 1 0.03
29 16 0.46
30 6 0.17
31 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTATAAAAATTAATAAATATATTAAAAA
Found at i:83718 original size:20 final size:20
Alignment explanation
Indices: 83605--83718 Score: 67
Period size: 20 Copynumber: 5.6 Consensus size: 20
83595 TACAAATTAT
*
83605 AAAATTATTAAAATT-TTAAA
1 AAAATTA-TAAATTTATTAAA
83625 AAAATTATAATATTT-TTATAA
1 AAAATTATAA-ATTTATTA-AA
*
83646 AAATTCTAATAAA-TTATT-AA
1 AAAAT-T-ATAAATTTATTAAA
* * *
83666 AAATTTATAAAATTAATAAA
1 AAAATTATAAATTTATTAAA
* *
83686 TCATATT-TAAAATTTATTAAA
1 -AAAATTAT-AAATTTATTAAA
83707 AAAATTATAAAT
1 AAAATTATAAAT
83719 AATAATAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.07
19 8 0.11
20 31 0.42
21 22 0.30
22 4 0.05
23 4 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTATAAATTTATTAAA
Found at i:83827 original size:10 final size:9
Alignment explanation
Indices: 83576--83866 Score: 74
Period size: 9 Copynumber: 29.9 Consensus size: 9
83566 TATTTTTCTC
*
83576 ATAAAAATC
1 ATAAAAATT
* *
83585 ACAAAAATC
1 ATAAAAATT
*
83594 ATACAAATT
1 ATAAAAATT
83603 AT-AAAATT
1 ATAAAAATT
*
83611 ATTAAAATTTT
1 A-TAAAA-ATT
*
83622 AAAAAAATT
1 ATAAAAATT
**
83631 ATAATATTTTT
1 ATAA-A-AATT
83642 ATAAAAATT
1 ATAAAAATT
*
83651 CTAATAAATT
1 ATAA-AAATT
83661 ATTAAAAATT
1 A-TAAAAATT
83671 -TATAAAATT
1 ATA-AAAATT
83680 AATAAATCATATT
1 -ATAAA--A-ATT
83693 -TAAAATTTATT
1 ATAAAA---ATT
*
83704 AAAAAAATT
1 ATAAAAATT
*
83713 ATAAATAATA
1 ATAAA-AATT
83723 ATAATAATATCT
1 ATAA-AA-AT-T
*
83735 AATAAAACATAA
1 -ATAAAA-AT-T
*
83747 AAAAAAATT
1 ATAAAAATT
* *
83756 GT-AATA-T
1 ATAAAAATT
83763 ATTAAAAATT
1 A-TAAAAATT
83773 AT--AAATT
1 ATAAAAATT
83780 ATAAGAAATT
1 ATAA-AAATT
*
83790 ATAAAACTT
1 ATAAAAATT
83799 AATAAAAATTTT
1 -ATAAAAA--TT
83811 ATAAAAAATT
1 AT-AAAAATT
**
83821 CATAAAACCT
1 -ATAAAAATT
* *
83831 ACAAATATT
1 ATAAAAATT
*
83840 GTAATAAATT
1 ATAA-AAATT
*
83850 AAAAAAATT
1 ATAAAAATT
83859 ATAAAAAT
1 ATAAAAAT
83867 AATTTCCAAA
Statistics
Matches: 206, Mismatches: 43, Indels: 66
0.65 0.14 0.21
Matches are distributed among these distances:
7 8 0.04
8 12 0.06
9 68 0.33
10 61 0.30
11 34 0.17
12 16 0.08
13 7 0.03
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:83870 original size:21 final size:21
Alignment explanation
Indices: 83846--83889 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
83836 TATTGTAATA
*
83846 AATTAAAAAAATTATAAAAAT
1 AATTAAAAAAATAATAAAAAT
***
83867 AATTTCCAAAATAATAAAAAT
1 AATTAAAAAAATAATAAAAAT
83888 AA
1 AA
83890 AACTTATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTAAAAAAATAATAAAAAT
Found at i:84034 original size:10 final size:9
Alignment explanation
Indices: 84005--84070 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
83995 TAACGAATCA
84005 TATAATAAAT
1 TATAA-AAAT
84015 TATAAAAAT
1 TATAAAAAT
*
84024 TATCAATAAT
1 TAT-AAAAAT
84034 TATAAAAAT
1 TATAAAAAT
* *
84043 AGTAAAAAAAA
1 --TATAAAAAT
*
84054 TATAAAACCT
1 TATAAAA-AT
84064 TATAAAA
1 TATAAAA
84071 TAAATTCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 18 0.40
10 20 0.44
11 7 0.16
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (9 bp):
TATAAAAAT
Found at i:84139 original size:23 final size:22
Alignment explanation
Indices: 84095--84163 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
84085 GTTCTAAGAA
* *
84095 ATTTATAAAAATTATAATTATT
1 ATTTATAAAAAATATAAATATT
*
84117 ATTTTTAAAAAATATAAA-A-T
1 ATTTATAAAAAATATAAATATT
* *
84137 A-TTA-AAAATATATAAAAATT
1 ATTTATAAAAAATATAAATATT
84157 CATTTAT
1 -ATTTAT
84164 TGGTTCCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 11 0.30
19 3 0.08
20 3 0.08
21 2 0.05
22 18 0.49
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTATAAAAAATATAAATATT
Found at i:91686 original size:11 final size:10
Alignment explanation
Indices: 91670--91707 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
91660 GCCACATTAG
91670 AAATTATTTAA
1 AAATTATTT-A
91681 AAATTA-TTA
1 AAATTATTTA
91690 AAATTATTTTA
1 AAATTA-TTTA
91701 AAATTAT
1 AAATTAT
91708 AATCACCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.28
10 3 0.12
11 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTATTTA
Found at i:91695 original size:20 final size:21
Alignment explanation
Indices: 91665--91707 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
91655 TATTTGCCAC
91665 ATTAGAAATTATTTAAAAATT
1 ATTAGAAATTATTTAAAAATT
*
91686 ATTA-AAATTATTTTAAAATT
1 ATTAGAAATTATTTAAAAATT
91706 AT
1 AT
91708 AATCACCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAGAAATTATTTAAAAATT
Found at i:92602 original size:17 final size:17
Alignment explanation
Indices: 92580--92612 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
92570 ATTATTTAAT
92580 TTTATATTTTAAAAAAG
1 TTTATATTTTAAAAAAG
92597 TTTATATTTTAAAAAA
1 TTTATATTTTAAAAAA
92613 ATAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTATATTTTAAAAAAG
Found at i:92925 original size:19 final size:19
Alignment explanation
Indices: 92884--92926 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
92874 TGCCAATTTT
** * *
92884 TTTTATAATTTTTATGAAT
1 TTTTATAAGCTTTATAAAA
92903 TTTTATAAGCTTTATAAAA
1 TTTTATAAGCTTTATAAAA
92922 TTTTA
1 TTTTA
92927 AATATACCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTATAAGCTTTATAAAA
Found at i:92961 original size:8 final size:8
Alignment explanation
Indices: 92943--93031 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
92933 CCAAATATGG
92943 TTTATTAAT
1 TTTA-TAAT
92952 TTTATAAT
1 TTTATAAT
92960 TTATAATAATT
1 TT-T-ATAA-T
92971 TTTATAAGTT
1 TTTATAA--T
92981 TTTATGAAATTT
1 TTTAT--AA--T
92993 TTTATAAT
1 TTTATAAT
93001 TTTATAAGT
1 TTTATAA-T
93010 TTATATAAAT
1 TT-TAT-AAT
*
93020 TTTAAAAT
1 TTTATAAT
93028 TTTA
1 TTTA
93032 AAATATTTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
8 21 0.30
9 14 0.20
10 20 0.29
11 5 0.07
12 9 0.13
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
TTTATAAT
Found at i:92975 original size:19 final size:18
Alignment explanation
Indices: 92951--93051 Score: 80
Period size: 19 Copynumber: 5.3 Consensus size: 18
92941 GGTTTATTAA
92951 TTTTATAATTTATAATAAT
1 TTTTATAATTT-TAATAAT
*
92970 TTTTATAAGTTTTTATGAAATT
1 TTTTATAA-TTTTAAT--AA-T
92992 TTTTATAATTTT-ATAAGT
1 TTTTATAATTTTAATAA-T
*
93010 TTATATAAATTTTAA-AAT
1 TTTTAT-AATTTTAATAAT
* *
93028 TTTAAAATATTTTAATAAT
1 TTTTATA-ATTTTAATAAT
93047 TTTTA
1 TTTTA
93052 ACAATTTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.01
18 19 0.28
19 26 0.39
20 6 0.09
21 6 0.09
22 9 0.13
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTATAATTTTAATAAT
Found at i:92982 original size:10 final size:9
Alignment explanation
Indices: 92951--93051 Score: 71
Period size: 10 Copynumber: 10.6 Consensus size: 9
92941 GGTTTATTAA
92951 TTTTATAAT
1 TTTTATAAT
*
92960 TTATAATAAT
1 TT-TTATAAT
92970 TTTTATAAGT
1 TTTTATAA-T
92980 TTTTATGAAATT
1 TTTTAT--AA-T
92992 TTTTATAA-
1 TTTTATAAT
93000 TTTTATAAGT
1 TTTTATAA-T
* *
93010 TTATATAAA
1 TTTTATAAT
*
93019 TTTTA-AAA
1 TTTTATAAT
*
93027 TTTTAAAAT
1 TTTTATAAT
93036 ATTTTAATAAT
1 -TTTT-ATAAT
93047 TTTTA
1 TTTTA
93052 ACAATTTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
8 16 0.21
9 14 0.19
10 32 0.43
11 4 0.05
12 9 0.12
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:93003 original size:20 final size:20
Alignment explanation
Indices: 92951--93051 Score: 65
Period size: 18 Copynumber: 5.2 Consensus size: 20
92941 GGTTTATTAA
92951 TTTTATAA-TTTATAATAAT
1 TTTTATAATTTTATAATAAT
*
92970 TTTTATAAGTTTTTATGAA-ATT
1 TTTTATAA--TTTTAT-AATAAT
*
92992 TTTTATAATTTTAT-A-AGT
1 TTTTATAATTTTATAATAAT
* *
93010 TTATATAAATTT-TAA-AA-
1 TTTTATAATTTTATAATAAT
*
93027 TTTTAAAATATTT-TAATAAT
1 TTTTATAAT-TTTATAATAAT
93047 TTTTA
1 TTTTA
93052 ACAATTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
17 7 0.11
18 21 0.32
19 10 0.15
20 11 0.17
22 15 0.23
23 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATAATTTTATAATAAT
Found at i:93006 original size:30 final size:30
Alignment explanation
Indices: 92965--93022 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
92955 ATAATTTATA
*
92965 ATAATTTTTATAAGTTTTTATGAAATTTTTT
1 ATAATTTTTATAAGTTTATAT-AAATTTTTT
92996 ATAA-TTTTATAAGTTTATATAAATTTT
1 ATAATTTTTATAAGTTTATATAAATTTT
93023 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
ATAATTTTTATAAGTTTATATAAATTTTTT
Found at i:93058 original size:19 final size:17
Alignment explanation
Indices: 93016--93059 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
93006 AAGTTTATAT
93016 AAATTTTAAAATTTTAA
1 AAATTTTAAAATTTTAA
93033 AATATTTTAATAATTTTTAA
1 AA-ATTTTAA-AA-TTTTAA
*
93053 CAATTTT
1 AAATTTT
93060 TTATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 7 0.30
20 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTTTAAAATTTTAA
Found at i:93067 original size:19 final size:20
Alignment explanation
Indices: 93018--93062 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
93008 GTTTATATAA
93018 ATTTTAA-AA-TTTTAAAAT
1 ATTTTAATAATTTTTAAAAT
93036 ATTTTAATAATTTTTAACAAT
1 ATTTTAATAATTTTTAA-AAT
*
93057 TTTTTA
1 ATTTTA
93063 TATTTATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 6 0.26
21 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAATAATTTTTAAAAT
Found at i:97874 original size:11 final size:11
Alignment explanation
Indices: 97854--97952 Score: 56
Period size: 11 Copynumber: 9.6 Consensus size: 11
97844 GATCGGGTCC
*
97854 AAATTCATTTT
1 AAATTTATTTT
97865 AAATTTATTTT
1 AAATTTATTTT
*
97876 -AA--GA-T-T
1 AAATTTATTTT
*
97882 AAATTTGTTTT
1 AAATTTATTTT
97893 AAA---ATTT-
1 AAATTTATTTT
97900 AAATTTATTTT
1 AAATTTATTTT
*
97911 AAATTTAAATTT
1 AAATTT-ATTTT
*
97923 -AATTTAAGTTT
1 AAATTT-ATTTT
97934 AAATTTATTTT
1 AAATTTATTTT
97945 CAAATTTA
1 -AAATTTA
97953 AAAGTATTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
6 1 0.01
7 6 0.09
8 4 0.06
10 7 0.10
11 34 0.50
12 16 0.24
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (11 bp):
AAATTTATTTT
Found at i:97901 original size:35 final size:34
Alignment explanation
Indices: 97862--97954 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 34
97852 CCAAATTCAT
**
97862 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAA
*
97897 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
97931 TTTAAATTTATTTTCAAATTTAAA
1 TTTAAATTTATTTT-AAATTTAAA
97955 AGTATTATAC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 17 0.32
35 36 0.68
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:97905 original size:6 final size:6
Alignment explanation
Indices: 97894--97954 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
97884 ATTTGTTTTA
* *
97894 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
97940 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
97955 AGTATTATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.29
6 28 0.62
7 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:97960 original size:18 final size:17
Alignment explanation
Indices: 97862--97954 Score: 125
Period size: 17 Copynumber: 5.4 Consensus size: 17
97852 CCAAATTCAT
97862 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
97880 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
97897 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
97914 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
97931 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
97949 TTTAAA
1 TTTAAA
97955 AGTATTATAC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
17 44 0.67
18 22 0.33
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:97969 original size:52 final size:52
Alignment explanation
Indices: 97862--97971 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
97852 CCAAATTCAT
* * ** *
97862 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAAGTATTATAAA
* * *
97914 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAAGTATTATACA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAAGTATTATAAA
97966 TTTAAA
1 TTTAAA
97972 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAAGTATTATAAA
Found at i:99901 original size:59 final size:59
Alignment explanation
Indices: 99834--100027 Score: 250
Period size: 59 Copynumber: 3.3 Consensus size: 59
99824 CCATAAATTA
*
99834 TCCAAAAATTCCATTTTTGACCCTAAAAGTTTCAAAATTTATATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAAGTTTCAAAATTTACATTTTTACCCTCGAACT
* * * * *
99893 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCTTCAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAAGTTTCAAAATTTACATTTTTACCCTCGAACT
* ** * *
99952 TCCAAAAATTCCATTTTTAACCC-CGAGGTCTCAAAATTTACCA-TTTTACCCTCGAA-T
1 TCCAAAAATTCCATTTTTGACCCTAAAAGTTTCAAAATTTA-CATTTTTACCCTCGAACT
100009 GTCCAAAAATTCCATTTTT
1 -TCCAAAAATTCCATTTTT
100028 ATCCCGATTT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
57 1 0.01
58 39 0.33
59 77 0.66
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCTAAAAGTTTCAAAATTTACATTTTTACCCTCGAACT
Found at i:100018 original size:30 final size:29
Alignment explanation
Indices: 99834--100028 Score: 173
Period size: 29 Copynumber: 6.7 Consensus size: 29
99824 CCATAAATTA
** *
99834 TCCAAAAATTCCATTTTTGACCCTAAAAGT
1 TCCAAAAATTCCATTTTT-ACCCTCGAACT
* * **
99864 TTCAAAATTTATATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
**
99893 TCCAAAAATTCCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTT-ACCCTCGAACT
* * *
99923 TCCAAAAATTACATTTTTACCTTCAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
**
99952 TCCAAAAATTCCATTTTTAACCC-CG-AGG
1 TCCAAAAATTCCATTTTT-ACCCTCGAACT
*
99980 TCTCAAAATTTACCA-TTTTACCCTCGAA-T
1 TC-CAAAAATT-CCATTTTTACCCTCGAACT
100009 GTCCAAAAATTCCATTTTTA
1 -TCCAAAAATTCCATTTTTA
100029 TCCCGATTTT
Statistics
Matches: 133, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
28 10 0.08
29 74 0.56
30 49 0.37
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCTCGAACT
Found at i:100051 original size:58 final size:57
Alignment explanation
Indices: 99834--100122 Score: 212
Period size: 59 Copynumber: 4.9 Consensus size: 57
99824 CCATAAATTA
* * * *
99834 TCCAAAAATTCCATTTTTGACCCTAAAAGTTTCAAAATTTA-TATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTAACCC-GAAA-TTTCAAAAATTACCA-TTTTACCCTCGAACT
* * * * *
99893 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTA-CATTTTTACCTTCAAACT
1 TCCAAAAATTCCATTTTTAACCC-GAAA-TTTCAAAAATTACCA-TTTTACCCTCGAACT
** * *
99952 TCCAAAAATTCCATTTTTAACCCCGAGGTCTCAAAATTTACCATTTTACCCTCGAA-T
1 TCCAAAAATTCCATTTTTAA-CCCGAAATTTCAAAAATTACCATTTTACCCTCGAACT
* ** * * *
100009 GTCCAAAAATTCCATTTTTATCCCGATTTTTCTAAAAATTACCGTTTTACCCTTGGA-T
1 -TCCAAAAATTCCATTTTTAACCCGAAATTTC-AAAAATTACCATTTTACCCTCGAACT
* * * *
100067 GT-CTAAAATTCCATTTTAAACCCTAAATTTTCCCAAAAA-TACCATTTTGCCCTCGA
1 -TCCAAAAATTCCATTTTTAACCCGAAA-TTT--CAAAAATTACCATTTTACCCTCGA
100123 GAATCCAAAA
Statistics
Matches: 190, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
57 28 0.15
58 78 0.41
59 80 0.42
60 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.37
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTTAACCCGAAATTTCAAAAATTACCATTTTACCCTCGAACT
Found at i:100140 original size:28 final size:28
Alignment explanation
Indices: 100099--100161 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
100089 CTAAATTTTC
100099 CCAAAAATACCATTTTGCCCTCGAGAAT
1 CCAAAAATACCATTTTGCCCTCGAGAAT
* * * *
100127 CCAAAATTATCATTTTGCCCTCGGGTAT
1 CCAAAAATACCATTTTGCCCTCGAGAAT
100155 CCAAAAA
1 CCAAAAA
100162 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (28 bp):
CCAAAAATACCATTTTGCCCTCGAGAAT
Found at i:100171 original size:29 final size:28
Alignment explanation
Indices: 100099--100171 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
100089 CTAAATTTTC
* *
100099 CCAAAAATACCATTTTGCCCTCGAGAAT
1 CCAAAAGTATCATTTTGCCCTCGAGAAT
* * *
100127 CCAAAATTATCATTTTGCCCTCGGGTAT
1 CCAAAAGTATCATTTTGCCCTCGAGAAT
*
100155 CCAAAAAGTCTCATTTT
1 CC-AAAAGTATCATTTT
100172 CAACTCCGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (28 bp):
CCAAAAGTATCATTTTGCCCTCGAGAAT
Found at i:105738 original size:6 final size:6
Alignment explanation
Indices: 105709--105799 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
105699 AGATACAATG
* * * * *
105709 AAGAAA AA-ATA AATAAA TAGAAA AAGAAA AA-AAA GAAGAAG AAGAAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA -AAGAAA AAGAAA
* * * *
105756 AAGAGA AAGAAA AA-AAA AAGCAAA AATAAG AAGAAA AACAAA AA
1 AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA AAGAAA AAGAAA AA
105800 TAGAAAAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
5 12 0.18
6 47 0.71
7 7 0.11
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:105767 original size:30 final size:29
Alignment explanation
Indices: 105730--105814 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
105720 AATAAATAGA
*
105730 AAAAGAAAAAAAAGAAGAAGAAGAAGAAG
1 AAAAGAAAAAAAAGAAGAAAAAGAAGAAG
*
105759 AGAAAGAAAAAAAA-AAGCAAAAATAAGAAG
1 A-AAAGAAAAAAAAGAAG-AAAAAGAAGAAG
*
105789 AAAA-ACAAAAATAGAA-AAAAAGAAGA
1 AAAAGA-AAAAAAAGAAGAAAAAGAAGA
105815 GGTCAAGGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
28 10 0.21
29 13 0.27
30 25 0.52
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (29 bp):
AAAAGAAAAAAAAGAAGAAAAAGAAGAAG
Found at i:105793 original size:25 final size:25
Alignment explanation
Indices: 105765--105814 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
105755 GAAGAGAAAG
105765 AAAA-AAAAA-AGCAAAAATAAGAAGA
1 AAAACAAAAATAG-AAAAA-AAGAAGA
105790 AAAACAAAAATAGAAAAAAAGAAGA
1 AAAACAAAAATAGAAAAAAAGAAGA
105815 GGTCAAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 11 0.48
26 10 0.43
27 2 0.09
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (25 bp):
AAAACAAAAATAGAAAAAAAGAAGA
Found at i:105804 original size:17 final size:18
Alignment explanation
Indices: 105768--105810 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
105758 GAGAAAGAAA
105768 AAAAAAAGCAAAAATAAG
1 AAAAAAAGCAAAAATAAG
105786 AAGAAAAA-CAAAAAT-AG
1 AA-AAAAAGCAAAAATAAG
105803 AAAAAAAG
1 AAAAAAAG
105811 AAGAGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 9 0.39
19 5 0.22
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAAAGCAAAAATAAG
Found at i:107171 original size:50 final size:50
Alignment explanation
Indices: 107015--107191 Score: 184
Period size: 50 Copynumber: 3.5 Consensus size: 50
107005 CATGAAGAAT
* * *
107015 GAAGGGAAAGGTTTAAGTCGCAACTGCAGGACCGTGTACCTCAGAAGACAC
1 GAAGGGAAAGGTTTAAGCCGCAACGGC-GGACCGTGTACCTCAGAAGACAA
* * * *
107066 GAAGGGAAAGATTTAAGCCTCAACGGCGGATCC-AGTA-CT-ATAAAGATACAA
1 GAAGGGAAAGGTTTAAGCCGCAACGGCGGA-CCGTGTACCTCA-GAAG--ACAA
* *
107117 -AAGGGAAAGGTTTAGGTCGCAACGGCGGACCGTGTACCTCAGAAGACAA
1 GAAGGGAAAGGTTTAAGCCGCAACGGCGGACCGTGTACCTCAGAAGACAA
107166 GAAGGG-AAGGATTTAAGCCGCAACGG
1 GAAGGGAAAGG-TTTAAGCCGCAACGG
107192 TGAATCTAGT
Statistics
Matches: 102, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
48 1 0.01
49 15 0.15
50 52 0.51
51 33 0.32
52 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (50 bp):
GAAGGGAAAGGTTTAAGCCGCAACGGCGGACCGTGTACCTCAGAAGACAA
Found at i:107212 original size:100 final size:101
Alignment explanation
Indices: 107016--107202 Score: 286
Period size: 100 Copynumber: 1.9 Consensus size: 101
107006 ATGAAGAATG
* *
107016 AAGGGAAAGGTTTAAGTCGCAACTGCAGGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
1 AAGGGAAAGGTTTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
* * *
107081 AGCCTCAACGGCGGATCCAGTACTATAAAGATACAA
66 AGCCGCAACGGCGAATCCAGTACTACAAAGATACAA
* *
107117 AAGGGAAAGGTTTAGGTCGCAACGGC-GGACCGTGTACCTCAGAAGACAAGAAGGGAAGGATTTA
1 AAGGGAAAGGTTTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
* *
107181 AGCCGCAACGGTGAATCTAGTA
66 AGCCGCAACGGCGAATCCAGTA
107203 TCACGAAGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 54 0.69
101 24 0.31
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.17
Consensus pattern (101 bp):
AAGGGAAAGGTTTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTA
AGCCGCAACGGCGAATCCAGTACTACAAAGATACAA
Found at i:107986 original size:115 final size:115
Alignment explanation
Indices: 107780--107987 Score: 292
Period size: 115 Copynumber: 1.8 Consensus size: 115
107770 GGCTCAAAGC
* ** * **
107780 GAGCAAATTTTCGAACCCTGGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAACAATAAAACGG
* *
107845 TTATCTTCCTGATAAGATACAGAGAAGTATACCAACTCAACGCTCGATAT
66 TTAGCTTCCTAATAAGATACAGAGAAGTATACCAACTCAACGCTCGATAT
* * *
107895 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGTTGAAACAATAAAATGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAACAATAAAACGG
*
107960 TTAGCTTCCTAATGAGATACTA-AGAAGT
66 TTAGCTTCCTAATAAGATAC-AGAGAAGT
107988 GGACTAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
115 79 0.99
116 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (115 bp):
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAACAATAAAACGG
TTAGCTTCCTAATAAGATACAGAGAAGTATACCAACTCAACGCTCGATAT
Found at i:108484 original size:206 final size:206
Alignment explanation
Indices: 108229--109072 Score: 1210
Period size: 206 Copynumber: 4.1 Consensus size: 206
108219 NNNNNNNNNN
* * *
108229 GATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGGTGAGCAAATCTTCGAATCCC-AACTT
1 GATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAA-CCCTAGCTT
* * *
108293 CCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAG
65 CCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTCCCTGATGAGATACTGAG
* * * * *
108358 AAGTAGACCAAATTTGTCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGACACGATCA
130 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACATGGTCA
*
108423 TCTTCCTAATGA
195 TCTTCCTGATGA
* *
108435 TATACTAAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAACCCTAGCTTC
1 GATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCTAGCTTC
* * * *
108500 CTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTGAGA
66 CTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTCCCTGATGAGATACTGAGA
* *
108565 AGTGGACCAAATACGTCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAACGACATGGTCAT
131 AGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACATGGTCAT
108630 CTTCCTGATGA
196 CTTCCTGATGA
* * * *
108641 GATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATGTTTGAACCCCAGCTTC
1 GATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCTAGCTTC
*
108706 CTGATGAGATACTAAGAAGCAGGTCGAAGAAATAAAATGGTTAGCTCCCTGATGAGATACTGAGA
66 CTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTCCCTGATGAGATACTGAGA
* *
108771 AGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAACGACGTGGTCAT
131 AGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACATGGTCAT
108836 CTTCCTGATGA
196 CTTCCTGATGA
* *
108847 GACAC-AGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCTTGCTT
1 GATACTA-AGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCTAGCTT
* * * * *
108911 CCTGATGAGATAATAAGAAGTAGATCGAAGCAATAAAGTGATTAGCTCCCTGATGAGATACTGAG
65 CCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTCCCTGATGAGATACTGAG
* * * * * * * **
108976 AAGTGAATCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCGAAA-AAA-GTGATGCAGT
130 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACATG--GT
*
109039 CACCTTCCTGATGA
193 CATCTTCCTGATGA
* *
109053 GATACTGAGAAGAAGGCCAA
1 GATACTAAGAAGAAGACCAA
109073 GTTAATGAAA
Statistics
Matches: 575, Mismatches: 58, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
204 3 0.01
205 6 0.01
206 566 0.98
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (206 bp):
GATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCTAGCTTC
CTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTCCCTGATGAGATACTGAGA
AGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACATGGTCAT
CTTCCTGATGA
Found at i:114970 original size:84 final size:84
Alignment explanation
Indices: 114881--115191 Score: 341
Period size: 84 Copynumber: 3.7 Consensus size: 84
114871 GAATAAGTTG
*
114881 AATAAATTTGTTTCAGGATTTATTCCCACCGTTCAACAGATTTAATTCTATATTTGGATTTTGGT
1 AATAAATTTGTTTCGGGATTTATTCCCACCGTTCAACAGATTTAATTCTATATTTGGATTTTGGT
114946 TCCAAATAATAATTAAGTA
66 TCCAAATAATAATTAAGTA
*** *
114965 AATAAATTTGTTTCGGGATTTATTCCCGTTGTTCAACAGATTTAATTCTATATTTGAATTTTGGT
1 AATAAATTTGTTTCGGGATTTATTCCCACCGTTCAACAGATTTAATTCTATATTTGGATTTTGGT
*
115030 TCCAAATAATGATTAAGTA
66 TCCAAATAATAATTAAGTA
* * * * * * *
115049 AATAAATATGTTTTGGGATTTATTCCCACTGTTTAACAGATTGT-ATTCCA-GTTT-GATTTTGT
1 AATAAATTTGTTTCGGGATTTATTCCCACCGTTCAACAGATT-TAATTCTATATTTGGATTTTGG
* *
115111 TTCCAATTAA-AA-TAAGTTG
65 TTCCAAATAATAATTAAG-TA
* * * * *
115130 ACTAAATCTATTTCGGGATTTATT-TCAGCCGATT-AACA-AATTATATTCTATATTTGGATTTT
1 AATAAATTTGTTTCGGGATTTATTCCCA-CCG-TTCAACAGATTTA-ATTCTATATTTGGATTTT
115192 ATAATAATTA
Statistics
Matches: 192, Mismatches: 27, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 8 0.04
81 33 0.17
82 20 0.10
83 9 0.05
84 120 0.62
85 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (84 bp):
AATAAATTTGTTTCGGGATTTATTCCCACCGTTCAACAGATTTAATTCTATATTTGGATTTTGGT
TCCAAATAATAATTAAGTA
Found at i:115530 original size:15 final size:15
Alignment explanation
Indices: 115510--115550 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
115500 GTTAGTGACT
115510 TTAAATTGTGAAAGC
1 TTAAATTGTGAAAGC
115525 TTAAATTGT---AGC
1 TTAAATTGTGAAAGC
115537 TTCAAATTGTGAAA
1 TT-AAATTGTGAAA
115551 TCAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.23
13 7 0.32
15 9 0.41
16 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (15 bp):
TTAAATTGTGAAAGC
Found at i:117524 original size:30 final size:30
Alignment explanation
Indices: 117490--117548 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
117480 AAAGTGTCCT
* *
117490 ACAACCACTTGGAAATGTGAGGGGTGTCTA
1 ACAACCACTTGAAAATGGGAGGGGTGTCTA
117520 ACAACCACTTGAAAATGGGAGGGGTGTCT
1 ACAACCACTTGAAAATGGGAGGGGTGTCT
117549 TGCTAACGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
ACAACCACTTGAAAATGGGAGGGGTGTCTA
Found at i:125179 original size:50 final size:51
Alignment explanation
Indices: 125085--125180 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
125075 TGTTTAATAA
* *
125085 ATTTTTTCAAATATGATGTTTTAAGTAAATATTAATATTTATTTAAAAGTG
1 ATTTTTTCAAATATGATGTTATAAGTAAATATAAATATTTATTTAAAAGTG
125136 ATTTGTTT-AAATATGATGTTATATA-TAAA-ATAAATATTTATTTAA
1 ATTT-TTTCAAATATGATGTTATA-AGTAAATATAAATATTTATTTAA
125181 TTGATTTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
50 15 0.37
51 22 0.54
52 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (51 bp):
ATTTTTTCAAATATGATGTTATAAGTAAATATAAATATTTATTTAAAAGTG
Found at i:129876 original size:29 final size:30
Alignment explanation
Indices: 129815--129887 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
129805 ACTTTTCTAG
* * *
129815 AGATTTGTCACAAAGGCTTTTGTTTAACAA
1 AGATTTGCCACAAAGGCTATTGTTAAACAA
129845 AGATTTGCCACAAAGGC-ATTGTTAAACAA
1 AGATTTGCCACAAAGGCTATTGTTAAACAA
*
129874 AGATTTTCCACAAA
1 AGATTTGCCACAAA
129888 ATCTTGTCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (30 bp):
AGATTTGCCACAAAGGCTATTGTTAAACAA
Found at i:130421 original size:42 final size:41
Alignment explanation
Indices: 130372--130482 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 41
130362 GGCTGTCGAC
*
130372 GCCACACAGTCGTGTACCAGGTTGTGTAGGGTACTGTTTTGA
1 GCCACACAGTCGTGTGCCAGGTTGTGTA-GGTACTGTTTTGA
* * * *
130414 GTCACACAATTGTGTGCCAGGCCATGTG-AGGTACTGTTTTGA
1 GCCACACAGTCGTGTGCCAGG--TTGTGTAGGTACTGTTTTGA
* * *
130456 GCCACAAAGCCGTGTGCCAGGTCGTGT
1 GCCACACAGTCGTGTGCCAGGTTGTGT
130483 GGGCCATAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
40 3 0.06
42 46 0.85
43 1 0.02
44 4 0.07
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.28
Consensus pattern (41 bp):
GCCACACAGTCGTGTGCCAGGTTGTGTAGGTACTGTTTTGA
Found at i:131891 original size:64 final size:63
Alignment explanation
Indices: 131815--132008 Score: 196
Period size: 64 Copynumber: 3.2 Consensus size: 63
131805 CATAAGACTT
131815 TATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATCAGTATTATATTGTTTA
1 TATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTAT-AGTATTATATTGTTTA
* * * ** * *
131879 TATTT-AATTTTAA-TTTA-TTTTTTAAGCTTTATAATTTA-GAGTT-TA--ATT-TA---CTT-
1 TATTTAAATTTAAACTCTATTTTTTTAGGAATAAT-ATTTAGGA-TTATAGTATTATATTGTTTA
131932 TATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATTAGTATTATATTGTTTA
1 TATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTA-TAGTATTATATTGTTTA
*
131996 TATTTAATTTTAA
1 TATTTAAATTTAA
132009 TTTATCTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
53 5 0.05
54 9 0.09
55 10 0.10
56 13 0.13
57 4 0.04
58 3 0.03
59 3 0.03
60 3 0.03
61 14 0.14
62 10 0.10
63 9 0.09
64 17 0.17
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.55
Consensus pattern (63 bp):
TATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATAGTATTATATTGTTTA
Found at i:131900 original size:62 final size:61
Alignment explanation
Indices: 131832--132018 Score: 185
Period size: 62 Copynumber: 3.1 Consensus size: 61
131822 ATTTAAACTC
131832 TATTTTTTTAGGAATAATATTTAGGATTATCAGTATTATATTGTTTATATTTAATTTTAATT
1 TATTTTTTTAGGAATAATATTTAGGATTAT-AGTATTATATTGTTTATATTTAATTTTAATT
* ** * * * * *
131894 TA-TTTTTTAAGCTTTATAATTTA-GAGTT-TA--ATT-TA--CTTTAT-TTAAATTTAAACTC
1 TATTTTTTTAGGAATAAT-ATTTAGGA-TTATAGTATTATATTGTTTATATTTAATTTTAA-TT
131949 TATTTTTTTAGGAATAATATTTAGGATTATTAGTATTATATTGTTTATATTTAATTTTAATT
1 TATTTTTTTAGGAATAATATTTAGGATTA-TAGTATTATATTGTTTATATTTAATTTTAATT
*
132011 TATCTTTT
1 TATTTTTT
132019 AAGCTTTATA
Statistics
Matches: 95, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
54 9 0.09
55 15 0.16
56 13 0.14
57 4 0.04
58 3 0.03
59 3 0.03
60 3 0.03
61 14 0.15
62 22 0.23
63 9 0.09
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (61 bp):
TATTTTTTTAGGAATAATATTTAGGATTATAGTATTATATTGTTTATATTTAATTTTAATT
Found at i:132001 original size:117 final size:117
Alignment explanation
Indices: 131811--132044 Score: 441
Period size: 117 Copynumber: 2.0 Consensus size: 117
131801 TTGACATAAG
131811 ACTTTATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATCAGTATTATATTGT
1 ACTTTATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATCAGTATTATATTGT
* *
131876 TTATATTTAATTTTAATTTATTTTTTAAGCTTTATAATTTAGAGTTTAATTT
66 TTATATTTAATTTTAATTTATCTTTTAAGCTTTATAATTTAGAGTTCAATTT
*
131928 ACTTTATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATTAGTATTATATTGT
1 ACTTTATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATCAGTATTATATTGT
131993 TTATATTTAATTTTAATTTATCTTTTAAGCTTTATAATTTAGAGTTCAATTT
66 TTATATTTAATTTTAATTTATCTTTTAAGCTTTATAATTTAGAGTTCAATTT
132045 GGATCCAACT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (117 bp):
ACTTTATTTAAATTTAAACTCTATTTTTTTAGGAATAATATTTAGGATTATCAGTATTATATTGT
TTATATTTAATTTTAATTTATCTTTTAAGCTTTATAATTTAGAGTTCAATTT
Found at i:133168 original size:21 final size:20
Alignment explanation
Indices: 133144--133188 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
133134 ATTCTTTCAG
133144 CATCATCTCTGCCTTTATCAA
1 CATCATCTCTGCC-TTATCAA
* *
133165 CATCCTCTTTGCCTTATCAA
1 CATCATCTCTGCCTTATCAA
133185 CATC
1 CATC
133189 CTTAGCCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.22, C:0.36, G:0.04, T:0.38
Consensus pattern (20 bp):
CATCATCTCTGCCTTATCAA
Found at i:135653 original size:77 final size:79
Alignment explanation
Indices: 135551--135743 Score: 234
Period size: 77 Copynumber: 2.5 Consensus size: 79
135541 TTTGGATTTT
* * ** *
135551 ATAATAATTAATTGAATAATTCTGTTTTAGGATTTATTCTTACTATTCAACAGA-A-TTGATTTG
1 ATAAGAATTAATTGAATAATTCTGTTTCAGGATTTATTCCCACCATTCAACAGATATTTGATTTG
135614 GATTTTGTTTCCAA
66 GATTTTGTTTCCAA
* *
135628 ATAAGAATTAATTGAATAATTCTGTTTCAAGATTTATTCCCACCATTCACCAGATTTGATTTGAT
1 ATAAGAATTAATTGAATAATTCTGTTTCAGGATTTATTCCCACCATTCAACAGA--T-ATTTGAT
*
135693 TTTGATTTTGTTTCCAA
63 TTGGATTTTGTTTCCAA
*
135710 ACAAAGAATTAATT--A-AATTCTGTTTCAGGATTTA
1 A-TAAGAATTAATTGAATAATTCTGTTTCAGGATTTA
135744 ATCCTTCCGT
Statistics
Matches: 100, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
77 47 0.47
80 18 0.18
81 2 0.02
82 22 0.22
83 11 0.11
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (79 bp):
ATAAGAATTAATTGAATAATTCTGTTTCAGGATTTATTCCCACCATTCAACAGATATTTGATTTG
GATTTTGTTTCCAA
Found at i:150062 original size:92 final size:91
Alignment explanation
Indices: 149752--150079 Score: 280
Period size: 92 Copynumber: 3.6 Consensus size: 91
149742 TAACATTTAA
* * * * ** *
149752 AAAAAAAAAAATAATTAAGCCTCTACTTTTATTTTGCACT-TTTTTGAATACTTGAACTTTCAAA
1 AAAAAAAAAAACAATTAAGCCACT-GTTTTTTTTTGCACTCAATTAG-ATACTTGAACTTTCAAA
* **
149816 ATGCATCAAAAAAACCCTTAATTTTTTTC
64 ATGCATC-AAAAAACCCTCAAACTTTTTC
* * * *
149845 ---AAAAAAACCAATTAAGCCTCTGTTTTTATTTTG----C-ATTGGGTACTTGAACTTTCAAAA
1 AAAAAAAAAAACAATTAAGCCACTGTTTTT-TTTTGCACTCAATTAGATACTTGAACTTTCAAAA
*
149902 TGCATCAAAAATACCCTCGAACTTTTTC
65 TGCATCAAAAA-ACCCTCAAACTTTTTC
* * * * *
149930 AAAAAAAAATAATAA-TAAGTCATTGCTTTTATTTTACACTCAATTAGATACTTGAACTTTCAAA
1 AAAAAAAAA-AACAATTAAGCCACTG-TTTTTTTTTGCACTCAATTAGATACTTGAACTTTCAAA
* *
149994 ATACATCGAAAAACCCTCAAACTTTTTC
64 ATGCATCAAAAAACCCTCAAACTTTTTC
* * * *
150022 AAAAAAAAAAGCAATTCAGCCCCTGATTTTTTTTTGCACTCAATTAGGTACTTGAACT
1 AAAAAAAAAAACAATTAAGCCACTG-TTTTTTTTTGCACTCAATTAGATACTTGAACT
150080 GTCCCTAATT
Statistics
Matches: 188, Mismatches: 33, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
84 5 0.03
85 35 0.19
86 3 0.02
88 17 0.09
89 11 0.06
90 24 0.13
91 3 0.02
92 60 0.32
93 30 0.16
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (91 bp):
AAAAAAAAAAACAATTAAGCCACTGTTTTTTTTTGCACTCAATTAGATACTTGAACTTTCAAAAT
GCATCAAAAAACCCTCAAACTTTTTC
Found at i:151529 original size:30 final size:32
Alignment explanation
Indices: 151462--151521 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
151452 AAAATTATAA
* *
151462 AATATAAAATTATATTTTGATCTTTTAAAAAT
1 AATAAAAAATTATATTTTAATCTTTTAAAAAT
151494 AATAAAAAATTA-A-TTTAATCTTTTAAAA
1 AATAAAAAATTATATTTTAATCTTTTAAAA
151522 CTTATAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 1 0.04
32 11 0.42
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (32 bp):
AATAAAAAATTATATTTTAATCTTTTAAAAAT
Found at i:163575 original size:82 final size:82
Alignment explanation
Indices: 163480--163644 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
163470 ATAAAATACA
163480 TAGACTAAATTCTAAATTTACGAAGAGTACGAGGACATATGATATATTTTAACCTATTTATTATC
1 TAGACTAAATTCTAAATTTACGAAGAGTACGAGGACATATGATATATTTTAACCTATTTATTATC
163545 TTTTGATTTGATCGGTT
66 TTTTGATTTGATCGGTT
*
163562 TAGACTAAATTCTAAATTTATGAAGAGTACGAGGACATATGATATATTTTAACCTATTTATTATC
1 TAGACTAAATTCTAAATTTACGAAGAGTACGAGGACATATGATATATTTTAACCTATTTATTATC
*
163627 TTTTGATTTTATCGGTT
66 TTTTGATTTGATCGGTT
163644 T
1 T
163645 TTATTATACA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (82 bp):
TAGACTAAATTCTAAATTTACGAAGAGTACGAGGACATATGATATATTTTAACCTATTTATTATC
TTTTGATTTGATCGGTT
Found at i:171805 original size:94 final size:93
Alignment explanation
Indices: 171626--171805 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
171616 TTAAAATAAG
** *
171626 TTTTAATAAATGGAACTATATATCTATAGTTTATTATAATAAAAATTAAAAAATAAATATGATTT
1 TTTTAATAAATAAAACTATATATCTATAGTTTATTATAATAAAAATTAAAAAATAAATATAATTT
171691 AAATCTCAAATAATATTACAGATATATC
66 AAATCTCAAATAATATTACAGATATATC
* * * * *
171719 TTTTAATAAATAAAATTATAT-TTTATATTTTCATTATGATAAAAATTTTAAAAAAT-TATATAA
1 TTTTAATAAATAAAACTATATATCTATAGTTT-ATTATAATAAAAA--TTAAAAAATAAATATAA
171782 TTTAAATCTCAAATAATATTACAG
63 TTTAAATCTCAAATAATATTACAG
171806 GCAGTTATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
92 8 0.11
93 30 0.39
94 29 0.38
95 9 0.12
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (93 bp):
TTTTAATAAATAAAACTATATATCTATAGTTTATTATAATAAAAATTAAAAAATAAATATAATTT
AAATCTCAAATAATATTACAGATATATC
Found at i:172984 original size:20 final size:20
Alignment explanation
Indices: 172961--173000 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
172951 TTATTCAAAC
*
172961 AATATTACT-TGAATATTTAT
1 AATATTA-TATGAATAATTAT
172981 AATATTATATGAATAATTAT
1 AATATTATATGAATAATTAT
173001 GTCTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
AATATTATATGAATAATTAT
Found at i:181535 original size:30 final size:30
Alignment explanation
Indices: 181499--181555 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
181489 TTTGTTTTAT
181499 TTCGTATTATATATAACTTTTATTTTTAAA
1 TTCGTATTATATATAACTTTTATTTTTAAA
*
181529 TTCGTATTATATCTAACTTTTATTTTT
1 TTCGTATTATATATAACTTTTATTTTT
181556 TTTGTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (30 bp):
TTCGTATTATATATAACTTTTATTTTTAAA
Found at i:181697 original size:23 final size:23
Alignment explanation
Indices: 181668--181718 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
181658 ATTATTTGTG
**
181668 TATGTATGTATAATTATGAATGC
1 TATGTATAAATAATTATGAATGC
* *
181691 TATGTATAAATAATTATGTATGT
1 TATGTATAAATAATTATGAATGC
181714 TATGT
1 TATGT
181719 TATTTTATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TATGTATAAATAATTATGAATGC
Found at i:181749 original size:21 final size:20
Alignment explanation
Indices: 181704--181807 Score: 92
Period size: 21 Copynumber: 5.3 Consensus size: 20
181694 GTATAAATAA
* *
181704 TTATGTATGTTAT-GTTATT
1 TTATGTATGTTATATTTACT
*
181723 TTATGTACGTTATATTTACT
1 TTATGTATGTTATATTTACT
*
181743 ATTATGTTTG-TATA-TT--T
1 -TTATGTATGTTATATTTACT
*
181760 GTATGTATGTTATATTTACT
1 TTATGTATGTTATATTTACT
*
181780 TCTATGTATGTTATGTTTACT
1 T-TATGTATGTTATATTTACT
181801 ATTATGT
1 -TTATGT
181808 TTGTATGACT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
16 7 0.10
17 5 0.07
18 2 0.03
19 14 0.21
20 9 0.13
21 30 0.44
22 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (20 bp):
TTATGTATGTTATATTTACT
Found at i:181772 original size:37 final size:36
Alignment explanation
Indices: 181709--181798 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 36
181699 AATAATTATG
181709 TATGTTATGTTATTTTATGTACGTTATATTTACTAT
1 TATGTTATGTTATTTTATGTACGTTATATTTACTAT
*
181745 TATGTT-TGTATATTTGTATGTATGTTATATTTACT-T
1 TATGTTATGT-TATTT-TATGTACGTTATATTTACTAT
181781 CTATG-TATGTTATGTTTA
1 -TATGTTATGTTAT-TTTA
181799 CTATTATGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
35 3 0.06
36 18 0.38
37 27 0.56
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.59
Consensus pattern (36 bp):
TATGTTATGTTATTTTATGTACGTTATATTTACTAT
Found at i:181787 original size:58 final size:56
Alignment explanation
Indices: 181705--181813 Score: 164
Period size: 58 Copynumber: 1.9 Consensus size: 56
181695 TATAAATAAT
*
181705 TATGTATGTTATGTTATTTTATGTACGTTATATTTACTATTATGTTTGTATATTTG
1 TATGTATGTTATGTTATTCTATGTACGTTATATTTACTATTATGTTTGTATATTTG
* * *
181761 TATGTATGTTATATTTACTTCTATGTATGTTATGTTTACTATTATGTTTGTAT
1 TATGTATGTTAT-GTTA-TTCTATGTACGTTATATTTACTATTATGTTTGTAT
181814 GACTGTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 12 0.26
57 3 0.06
58 32 0.68
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.59
Consensus pattern (56 bp):
TATGTATGTTATGTTATTCTATGTACGTTATATTTACTATTATGTTTGTATATTTG
Found at i:184731 original size:18 final size:18
Alignment explanation
Indices: 184710--184747 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
184700 AGCTCCTTCA
184710 ACACAACAAACTCCTCCT
1 ACACAACAAACTCCTCCT
184728 ACACAACAAACTCCTCCT
1 ACACAACAAACTCCTCCT
184746 AC
1 AC
184748 CATGTCACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (18 bp):
ACACAACAAACTCCTCCT
Found at i:185120 original size:23 final size:23
Alignment explanation
Indices: 185094--185141 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
185084 CATAGAGATA
185094 GTTTT-TTTAACATACGATGGATG
1 GTTTTATTT-ACATACGATGGATG
* *
185117 GTTTTATTTAGATACGGTGGATG
1 GTTTTATTTACATACGATGGATG
185140 GT
1 GT
185142 CTTGGTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.23, C:0.06, G:0.27, T:0.44
Consensus pattern (23 bp):
GTTTTATTTACATACGATGGATG
Found at i:186408 original size:29 final size:29
Alignment explanation
Indices: 186353--186409 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
186343 CCAATGCACG
* * *
186353 AAAAAAAAGTTCAGGTATCTATCTGGGAA
1 AAAAAAAACTTCAGGTACCAATCTGGGAA
* *
186382 AAAAAAAACTTTAGGTACCAATTTGGGA
1 AAAAAAAACTTCAGGTACCAATCTGGGA
186410 GAAGTGGACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (29 bp):
AAAAAAAACTTCAGGTACCAATCTGGGAA
Found at i:187313 original size:41 final size:41
Alignment explanation
Indices: 187267--187352 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
187257 ATGACCTAGA
* *
187267 CACACGCTCGTATGTTAGCTCATGTGCCTCACATGGTTTGG
1 CACACGCTCGTATGTCAGCTCATGTGCCTCACATAGTTTGG
* *
187308 CACACGCTCGTTTGTCAGCTCGTGTGCCTCACATAGTTTGG
1 CACACGCTCGTATGTCAGCTCATGTGCCTCACATAGTTTGG
187349 CACA
1 CACA
187353 TACCCGTGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.30
Consensus pattern (41 bp):
CACACGCTCGTATGTCAGCTCATGTGCCTCACATAGTTTGG
Found at i:188908 original size:15 final size:15
Alignment explanation
Indices: 188888--188921 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
188878 CTTTCCCATC
188888 AATCACATTATT-AGG
1 AATCACATT-TTAAGG
188903 AATCACATTTTAAGG
1 AATCACATTTTAAGG
188918 AATC
1 AATC
188922 GTATTCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (15 bp):
AATCACATTTTAAGG
Found at i:189957 original size:7 final size:7
Alignment explanation
Indices: 189932--189968 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
189922 AGATCAAATT
189932 ATATTAA
1 ATATTAA
* *
189939 AAATTTA
1 ATATTAA
189946 ATATTAA
1 ATATTAA
189953 ATATTAA
1 ATATTAA
189960 ATATTAA
1 ATATTAA
189967 AT
1 AT
189969 CTCAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATTAA
Found at i:189975 original size:21 final size:21
Alignment explanation
Indices: 189932--189980 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
189922 AGATCAAATT
* *
189932 ATATTAAAAATTTAATATTAA
1 ATATTAAAAATTAAATATCAA
* *
189953 ATATTAAATATTAAATCTCAA
1 ATATTAAAAATTAAATATCAA
189974 AT-TTAAA
1 ATATTAAA
189981 CATAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATTAAAAATTAAATATCAA
Found at i:190169 original size:75 final size:74
Alignment explanation
Indices: 190072--190224 Score: 270
Period size: 75 Copynumber: 2.1 Consensus size: 74
190062 GCATCAACAT
*
190072 TATTGCATTAATTCGATATTTATTTATTTAATTCTTTGGTTCCCACTTTAACTCTAACCAAACAA
1 TATTGCATTAATTCGATATTTATTTATTTAATTCTTTGGTTCCCACTTTAACGCTAACCAAACAA
190137 TGTCATAAA
66 TGTCATAAA
* *
190146 TATTGCAATTAGTTCGGTATTTATTTATTTAATTCTTTGGTTCCCACTTTAACGCTAACCAAACA
1 TATTGC-ATTAATTCGATATTTATTTATTTAATTCTTTGGTTCCCACTTTAACGCTAACCAAACA
190211 ATGTCATAAA
65 ATGTCATAAA
190221 TATT
1 TATT
190225 CCTTCCAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 6 0.08
75 69 0.92
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.43
Consensus pattern (74 bp):
TATTGCATTAATTCGATATTTATTTATTTAATTCTTTGGTTCCCACTTTAACGCTAACCAAACAA
TGTCATAAA
Found at i:196861 original size:3 final size:3
Alignment explanation
Indices: 196853--196892 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
196843 AGATCACAAC
196853 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
196893 CATCATCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:203191 original size:17 final size:17
Alignment explanation
Indices: 203169--203230 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
203159 TTGGAAATTG
* *
203169 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTTGA
203186 AATTTAAATTTA-TTGA
1 AATTTAAATTTATTTGA
203202 AATTTAAATTTATTATGA
1 AATTTAAATTTATT-TGA
203220 AA-TTAAATTTA
1 AATTTAAATTTA
203231 GAAAAGTCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.37
17 21 0.51
18 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:203207 original size:33 final size:32
Alignment explanation
Indices: 203165--203230 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
203155 CTAGTTGGAA
* *
203165 ATTGAATTTAAGTTTATT-TTAAATTTAAATTT
1 ATTGAATTTAAATTTATTATGAAA-TTAAATTT
203197 ATTGAAATTTAAATTTATTATGAAATTAAATTT
1 ATTG-AATTTAAATTTATTATGAAATTAAATTT
203230 A
1 A
203231 GAAAAGTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 4 0.13
33 22 0.73
34 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (32 bp):
ATTGAATTTAAATTTATTATGAAATTAAATTT
Found at i:203344 original size:15 final size:15
Alignment explanation
Indices: 203270--203338 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
203260 CAAAAGTCCA
203270 AATTACAAATGGCCC
1 AATTACAAATGGCCC
*
203285 AATAACAAATGGCCC
1 AATTACAAATGGCCC
* * *
203300 AGTTACAGATGACCC
1 AATTACAAATGGCCC
*
203315 AAATACAAATGGCCC
1 AATTACAAATGGCCC
203330 AATTACAAA
1 AATTACAAA
203339 GTGCCCGAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.17
Consensus pattern (15 bp):
AATTACAAATGGCCC
Done.