Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007927.1 Hibiscus syriacus cultivar Beakdansim tig00110333_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 706544
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:13125 original size:19 final size:19
Alignment explanation
Indices: 13101--13153 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
13091 AACTGAAACC
13101 GGTTTTTTGGTTCGGTTCG
1 GGTTTTTTGGTTCGGTTCG
**
13120 GGTTTTTT--AACGGTTCG
1 GGTTTTTTGGTTCGGTTCG
*
13137 GGTTTTTCGGTTCGGTT
1 GGTTTTTTGGTTCGGTT
13154 TTTCAATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.52
19 13 0.48
ACGTcount: A:0.04, C:0.11, G:0.34, T:0.51
Consensus pattern (19 bp):
GGTTTTTTGGTTCGGTTCG
Found at i:28279 original size:20 final size:20
Alignment explanation
Indices: 28254--28291 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28244 TATGAGTATA
28254 TTGTATAATATAGTATAGTT
1 TTGTATAATATAGTATAGTT
**
28274 TTGTATTGTATAGTATAG
1 TTGTATAATATAGTATAG
28292 AATTGTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
TTGTATAATATAGTATAGTT
Found at i:31596 original size:31 final size:31
Alignment explanation
Indices: 31548--31670 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
31538 CCCGAAGGAC
* * *
31548 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
31579 CAGCCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
31610 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
31641 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
31671 CCCTCGACCC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:32503 original size:21 final size:21
Alignment explanation
Indices: 32473--32517 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
32463 ATTCTGGCGT
32473 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
32494 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
32515 TTG
1 TTG
32518 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:35417 original size:20 final size:19
Alignment explanation
Indices: 35392--35429 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
35382 ATTGTTATGT
35392 AGAGAAAAAAATGGGAAAAA
1 AGAGAAAAAAAT-GGAAAAA
*
35412 AGAGAAAATAATGGAAAA
1 AGAGAAAAAAATGGAAAA
35430 GGCAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
AGAGAAAAAAATGGAAAAA
Found at i:37894 original size:30 final size:30
Alignment explanation
Indices: 37858--37944 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
37848 TTGGTTTTTA
*
37858 AAAAAATAATTTACATAAAATTAATTACTT
1 AAAAAATAATTTACATAAAATAAATTACTT
* * *
37888 AAAAAATATTTTACGTAAAATAAATTACAT
1 AAAAAATAATTTACATAAAATAAATTACTT
* * * **
37918 ACAAATTATTTTATGTAAAATAAATTA
1 AAAAAATAATTTACATAAAATAAATTA
37945 TATCTTCTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAAATAATTTACATAAAATAAATTACTT
Found at i:39294 original size:2 final size:2
Alignment explanation
Indices: 39287--39326 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39277 TTACATAAAC
39287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39327 TGTGTGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39855 original size:21 final size:19
Alignment explanation
Indices: 39822--39926 Score: 64
Period size: 18 Copynumber: 5.7 Consensus size: 19
39812 TTAAAATTTT
39822 TATATATTAAATATTATAA
1 TATATATTAAATATTATAA
*
39841 TATATATTACTAATAAAATATAA
1 TATATATTA--AAT--ATTATAA
39864 TAT-TATTAAAATATT-TAA
1 TATATATT-AAATATTATAA
* *
39882 -ATATATT---CATTAAAA
1 TATATATTAAATATTATAA
* *
39897 T-TATATCAAATATTATAT
1 TATATATTAAATATTATAA
39915 TA-ATATTAAATA
1 TATATATTAAATA
39927 AATAAAATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 25
0.66 0.09 0.25
Matches are distributed among these distances:
14 3 0.05
15 7 0.11
17 2 0.03
18 22 0.34
19 11 0.17
21 6 0.09
22 4 0.06
23 10 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATATTAAATATTATAA
Found at i:39909 original size:22 final size:20
Alignment explanation
Indices: 39862--39912 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
39852 AATAAAATAT
*
39862 AATATTATTAAAATATTTAA
1 AATATTATTAAAATATATAA
*
39882 ATATATTCATTAAAATTATATCA
1 A-ATATT-ATTAAAA-TATATAA
39905 AATATTAT
1 AATATTAT
39913 ATTAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 7 0.27
22 12 0.46
23 6 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTATTAAAATATATAA
Found at i:62707 original size:2 final size:2
Alignment explanation
Indices: 62700--62792 Score: 85
Period size: 2 Copynumber: 50.5 Consensus size: 2
62690 CTGCCCCGAT
* *
62700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
62742 T- TA -A T- TA TA TA TA TA -A TA T- TT TA TA TT TT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62778 -A T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
62793 TTTCGGGTTC
Statistics
Matches: 76, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
1 8 0.11
2 68 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:63410 original size:22 final size:22
Alignment explanation
Indices: 63345--63410 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
63335 AGTCATCTCA
* *
63345 ATTCATAATGAATAATTATACCT
1 ATTCAT-ATGAATAATCACACCT
* *
63368 AATCATATGAATCAA-CGCACCT
1 ATTCATATGAAT-AATCACACCT
63390 ATTCATATGAATAATCACACC
1 ATTCATATGAATAATCACACC
63411 ACTTAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.06
22 26 0.74
23 7 0.20
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (22 bp):
ATTCATATGAATAATCACACCT
Found at i:71064 original size:20 final size:19
Alignment explanation
Indices: 71023--71063 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
71013 ATTTCAGTCA
*
71023 TTTGAGGTATGTTTTTGTT
1 TTTGAGGTAAGTTTTTGTT
71042 TTTGAGGTAAAGTTTTT-TT
1 TTTGAGGT-AAGTTTTTGTT
71061 TTT
1 TTT
71064 TTGGGTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.15, C:0.00, G:0.22, T:0.63
Consensus pattern (19 bp):
TTTGAGGTAAGTTTTTGTT
Found at i:76746 original size:15 final size:15
Alignment explanation
Indices: 76726--76762 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
76716 ATATTTAGCT
*
76726 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
76741 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
76756 GGGCGGG
1 GGGCGGG
76763 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:78817 original size:17 final size:19
Alignment explanation
Indices: 78784--78822 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
78774 TTCATTCTGT
*
78784 CTTATTATTTAATTCCA-A
1 CTTATCATTTAATTCCAGA
78802 CTTATCATTT-ATTCCAGA
1 CTTATCATTTAATTCCAGA
78820 CTT
1 CTT
78823 TTCAAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.49
Consensus pattern (19 bp):
CTTATCATTTAATTCCAGA
Found at i:79369 original size:25 final size:26
Alignment explanation
Indices: 79341--79394 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
79331 CATCCTAGAA
*
79341 CATA-AGG-GTATTTTCATAATTTTAC
1 CATACAGGAGTATTCTCATAATTTT-C
*
79366 CATACCGGAGTATTCTCATAATTTTC
1 CATACAGGAGTATTCTCATAATTTTC
79392 CAT
1 CAT
79395 CCAAGTGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 6 0.24
27 15 0.60
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (26 bp):
CATACAGGAGTATTCTCATAATTTTC
Found at i:92316 original size:22 final size:22
Alignment explanation
Indices: 92291--92332 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
92281 GTCCAATAAA
92291 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
92313 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
92333 AGGCCGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCGG
Found at i:96352 original size:19 final size:19
Alignment explanation
Indices: 96312--96354 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
96302 TTTTTAAAAA
*
96312 TAAAACAAAAAATAATTTT
1 TAAAACAAAAAATAATTAT
*
96331 TAAAATAAAAAATACA-TAT
1 TAAAACAAAAAATA-ATTAT
96350 TAAAA
1 TAAAA
96355 AAACTAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAACAAAAAATAATTAT
Found at i:96687 original size:13 final size:13
Alignment explanation
Indices: 96669--96694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96659 TTCCAAATTT
96669 ATCGGAATTGAAA
1 ATCGGAATTGAAA
96682 ATCGGAATTGAAA
1 ATCGGAATTGAAA
96695 TAGAATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
ATCGGAATTGAAA
Found at i:101374 original size:21 final size:22
Alignment explanation
Indices: 101327--101374 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
101317 AGTTGTTGGA
101327 GCTTCATAACTCTCTGGTTCTT
1 GCTTCATAACTCTCTGGTTCTT
*
101349 G-TTCATAA-TGTACTGGTTC-T
1 GCTTCATAACTCT-CTGGTTCTT
101369 GCTTCA
1 GCTTCA
101375 GAAGAATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 18 0.78
22 1 0.04
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (22 bp):
GCTTCATAACTCTCTGGTTCTT
Found at i:104119 original size:13 final size:13
Alignment explanation
Indices: 104073--104108 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
104063 ACCCGACCCG
* *
104073 ACCCGACTCGTTT
1 ACCCGACCCGTTC
104086 ACCCGACCCGTTC
1 ACCCGACCCGTTC
104099 ACCCGACCCG
1 ACCCGACCCG
104109 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTC
Found at i:106632 original size:24 final size:24
Alignment explanation
Indices: 106605--106665 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
106595 ATTTCAAATT
* *
106605 TGGATTCTGTTATGATACCTGACC
1 TGGATTCTGATATGATACATGACC
*
106629 TGGATTCTGATCTGATACATGACC
1 TGGATTCTGATATGATACATGACC
106653 TGGATTCTGATAT
1 TGGATTCTGATAT
106666 AATATACTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (24 bp):
TGGATTCTGATATGATACATGACC
Found at i:106802 original size:35 final size:35
Alignment explanation
Indices: 106755--106829 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
106745 TGGAGGAAGA
*
106755 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
106790 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
106825 TTACT
1 TTACT
106830 GTTCGTGACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.09, C:0.29, G:0.28, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:111320 original size:24 final size:24
Alignment explanation
Indices: 111293--111363 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
111283 ATTTCAAATT
* *
111293 TGGATTCTGTTATGATACCTGACC
1 TGGATTCTGATATGATACATGACC
* *
111317 TGGATTTTGATCTGATACATGACC
1 TGGATTCTGATATGATACATGACC
* *
111341 TGGATTCTGATATAATACTTGAC
1 TGGATTCTGATATGATACATGAC
111364 TTGAATTATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
TGGATTCTGATATGATACATGACC
Found at i:116850 original size:18 final size:19
Alignment explanation
Indices: 116827--116869 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
116817 AAATAATAAT
* *
116827 ATAAAT-TTTTAGAGAAGA
1 ATAAATATTTAAGAGAAAA
116845 ATAAATAATTTAAGAGAAAA
1 ATAAAT-ATTTAAGAGAAAA
116865 ATAAA
1 ATAAA
116870 GACTAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (19 bp):
ATAAATATTTAAGAGAAAA
Found at i:118318 original size:42 final size:41
Alignment explanation
Indices: 118238--118318 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
118228 AAAAAAATAT
* * ***
118238 TAAATTATATTTTTTCTATTTAGATATTTAATTTTTTTTGG
1 TAAATTATATTTTTTCTATCTAGATATCTAAACATTTTTGG
*
118279 TAAATTATATTTATTTTTATCTAGATATCTAAACATTTTT
1 TAAATTATATTT-TTTCTATCTAGATATCTAAACATTTTT
118319 TTCAATATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 12 0.36
42 21 0.64
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (41 bp):
TAAATTATATTTTTTCTATCTAGATATCTAAACATTTTTGG
Found at i:125785 original size:14 final size:14
Alignment explanation
Indices: 125745--125799 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 14
125735 ATTTTTATGA
125745 TTAAAATTT-TTAT
1 TTAAAATTTATTAT
125758 TTATAACATCTTATTAT
1 TTA-AA-AT-TTATTAT
125775 TTAAAATTTATTAT
1 TTAAAATTTATTAT
125789 TAGTAAAATTT
1 T--TAAAATTT
125800 TTGAGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.08
14 10 0.28
15 4 0.11
16 12 0.33
17 7 0.19
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (14 bp):
TTAAAATTTATTAT
Found at i:126539 original size:33 final size:33
Alignment explanation
Indices: 126496--126561 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
126486 ATATTATATT
* * * *
126496 CAAATTGACAAACTCATACCATGACCATATAGC
1 CAAATCGACAAAATCACACCATAACCATATAGC
126529 CAAATCGACAAAATCACACCATAACCATATAGC
1 CAAATCGACAAAATCACACCATAACCATATAGC
126562 TGAAAGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.29, G:0.08, T:0.18
Consensus pattern (33 bp):
CAAATCGACAAAATCACACCATAACCATATAGC
Found at i:126608 original size:2 final size:2
Alignment explanation
Indices: 126601--126636 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
126591 TTATATTACC
126601 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126637 TTTCATATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:132304 original size:162 final size:158
Alignment explanation
Indices: 132132--132458 Score: 582
Period size: 162 Copynumber: 2.0 Consensus size: 158
132122 AATCCTCGTC
* *
132132 CCCGACCTGAATCCCGACGGTTTTTTATCGGGACGTCCCGTCGAGGATTTTTTTTGTCCTGTCTC
1 CCCGACCTGAATCCCGACGGTTTTTTATCGGGACGTCCCGTCGAGGATTTTTTTTGTCCCGTCCC
132197 CGAACCCAAAAATATTTTATATATAATTAATATAAAAATAAAAAATATTATATATATATATATAT
66 CGAACCCAAAAATATTTTATATATAATTAATATAAAAAT-AAAAA-A-TAT-TATATATATATAT
132262 ATATAATAGGGGCGGGGATACCTTGCCCCGAA
127 ATATAATAGGGGCGGGGATACCTTGCCCCGAA
132294 CCCGACCTGAATCCCGACGGTTTTTTATCGGGACGTCCCGTCGAGGATTTTTTTTGTCCCGTCCC
1 CCCGACCTGAATCCCGACGGTTTTTTATCGGGACGTCCCGTCGAGGATTTTTTTTGTCCCGTCCC
*
132359 CGAACCCGAAAATATTTTATATATAATTAATATAAAAATAAAAAATATTATATATATATATATAT
66 CGAACCCAAAAATATTTTATATATAATTAATATAAAAATAAAAAATATTATATATATATATATAT
*
132424 AATCGGGGCGGGGATACCTTGCCCCGAA
131 AATAGGGGCGGGGATACCTTGCCCCGAA
132452 CCCGACC
1 CCCGACC
132459 CGAAAAAAAT
Statistics
Matches: 161, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
158 51 0.32
159 3 0.02
160 1 0.01
161 5 0.03
162 101 0.63
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (158 bp):
CCCGACCTGAATCCCGACGGTTTTTTATCGGGACGTCCCGTCGAGGATTTTTTTTGTCCCGTCCC
CGAACCCAAAAATATTTTATATATAATTAATATAAAAATAAAAAATATTATATATATATATATAT
AATAGGGGCGGGGATACCTTGCCCCGAA
Found at i:137755 original size:35 final size:35
Alignment explanation
Indices: 137709--137778 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
137699 GTGACTAATA
137709 ATTCTCACTTACGTAGGTTATTTCATCAAGTTTAT
1 ATTCTCACTTACGTAGGTTATTTCATCAAGTTTAT
137744 ATTCTCACTTACGTAGGTTATTTCATCAAGTTTAT
1 ATTCTCACTTACGTAGGTTATTTCATCAAGTTTAT
137779 CTCAATGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (35 bp):
ATTCTCACTTACGTAGGTTATTTCATCAAGTTTAT
Found at i:151590 original size:3 final size:3
Alignment explanation
Indices: 151577--151645 Score: 75
Period size: 3 Copynumber: 21.3 Consensus size: 3
151567 ATAAAAAATA
*
151577 AAT AAT AAAT AAT AAT AAAT AAT AAT AAT AAT AGAT AAT AAT AGT AAT
1 AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
151625 AGT AAT AAT AAAT AAAT AAT A
1 AAT AAT AAT -AAT -AAT AAT A
151646 TTTTTTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
3 42 0.72
4 16 0.28
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:151592 original size:10 final size:10
Alignment explanation
Indices: 151559--151645 Score: 88
Period size: 10 Copynumber: 8.4 Consensus size: 10
151549 CACCTACAAA
*
151559 AATAAAAAAT
1 AATAAATAAT
*
151569 AAAAAATAAAT
1 AATAAAT-AAT
151580 AATAAATAAT
1 AATAAATAAT
151590 AATAAATAAT
1 AATAAATAAT
151600 AAT-AATAAT
1 AATAAATAAT
151609 AGAT-AATAAT
1 A-ATAAATAAT
*
151619 AGTAATAGTAAT
1 AATAA-A-TAAT
151631 AATAAATAAAT
1 AATAAAT-AAT
151642 AATA
1 AATA
151646 TTTTTTTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
9 8 0.12
10 32 0.48
11 18 0.27
12 8 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
AATAAATAAT
Found at i:151645 original size:7 final size:7
Alignment explanation
Indices: 151559--151639 Score: 69
Period size: 7 Copynumber: 11.3 Consensus size: 7
151549 CACCTACAAA
*
151559 AATAAAA
1 AATAAAT
*
151566 AATAAAA
1 AATAAAT
151573 AATAAAT
1 AATAAAT
151580 AATAAAT
1 AATAAAT
151587 AAT-AAT
1 AATAAAT
151593 AA-ATAAT
1 AATA-AAT
151600 AAT-AAT
1 AATAAAT
*
151606 AATAGAT
1 AATAAAT
151613 AATAATAGT
1 AATAA-A-T
151622 AATAGTAAT
1 AATA--AAT
151631 AATAAAT
1 AATAAAT
151638 AA
1 AA
151640 ATAATATTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
6 11 0.17
7 39 0.62
8 1 0.02
9 10 0.16
10 1 0.02
11 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (7 bp):
AATAAAT
Found at i:152127 original size:106 final size:106
Alignment explanation
Indices: 151997--152910 Score: 1506
Period size: 106 Copynumber: 8.6 Consensus size: 106
151987 AGTATTGTTC
* * ** * * * *
151997 CGAGTCCAATATCATCCACTGTGAAGTTGAAATTGGTTCTGAAACTG-GAAAATTGTTTATTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGAC
* * **
152061 AACCAGCGGTCCCTTCGTTGTGAAGTAGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
* *
152103 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
152168 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
* * *
152209 GGAGTCAAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
152274 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
* * * *
152315 GGAGTTCAATATCCTTCGTTGTAAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
* *
152380 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
152421 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
* *
152486 ACCAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
152527 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
*
152592 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
* * * * *
152633 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
*
152698 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
152739 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
* *
152804 ACCATCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
152845 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
152910 A
66 A
152911 ACAACTTTTC
Statistics
Matches: 765, Mismatches: 42, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
106 764 1.00
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
Found at i:158485 original size:11 final size:11
Alignment explanation
Indices: 158469--158506 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
158459 GCACCTACAA
158469 AAATAAAAAAT
1 AAATAAAAAAT
*
158480 AAATAATAAAT
1 AAATAAAAAAT
*
158491 -AATAAATAAT
1 AAATAAAAAAT
158501 AAATAA
1 AAATAA
158507 TAATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:158494 original size:3 final size:3
Alignment explanation
Indices: 158481--158556 Score: 80
Period size: 3 Copynumber: 23.3 Consensus size: 3
158471 ATAAAAAATA
158481 AAT AAT AAAT AAT AAAT AAT AAAT AAT AAT AAT AAT AAT AGAT AAT AAT
1 AAT AAT -AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
158530 AGT AAT AGT AAT AAT AAAT AAAT AAT A
1 AAT AAT AAT AAT AAT -AAT -AAT AAT A
158557 TTTTTTAAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
3 45 0.70
4 19 0.30
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:158556 original size:7 final size:7
Alignment explanation
Indices: 158470--158550 Score: 94
Period size: 7 Copynumber: 11.3 Consensus size: 7
158460 CACCTACAAA
*
158470 AATAAAA
1 AATAAAT
158477 AATAAAT
1 AATAAAT
158484 AATAAAT
1 AATAAAT
158491 AATAAAT
1 AATAAAT
158498 AATAAAT
1 AATAAAT
158505 AAT-AAT
1 AATAAAT
158511 AAT-AAT
1 AATAAAT
*
158517 AATAGAT
1 AATAAAT
158524 AATAATAGT
1 AATAA-A-T
158533 AATAGTAAT
1 AATA--AAT
158542 AATAAAT
1 AATAAAT
158549 AA
1 AA
158551 ATAATATTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
6 12 0.18
7 41 0.62
8 1 0.02
9 10 0.15
10 1 0.02
11 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:162801 original size:15 final size:15
Alignment explanation
Indices: 162781--162825 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
162771 TAATAATTTT
*
162781 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
162796 ATTTATTATAAAATA
1 ATTTATTATAAAATA
162811 ATTTATTATAAAATA
1 ATTTATTATAAAATA
162826 TGGATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:162851 original size:15 final size:15
Alignment explanation
Indices: 162781--162852 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
162771 TAATAATTTT
*
162781 ATTTATTTTAAAATA
1 ATTTATTTAAAAATA
162796 ATTTA-TTATAAAATA
1 ATTTATTTA-AAAATA
162811 ATTTATTATAAAATATGGATTA
1 ATTTATT-T-AAA-A---A-TA
162833 ATTTATTTAAAAATA
1 ATTTATTTAAAAATA
162848 ATTTA
1 ATTTA
162853 GTAGTATGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 18
0.71 0.02 0.27
Matches are distributed among these distances:
14 2 0.04
15 23 0.49
16 2 0.04
17 3 0.06
18 2 0.04
19 1 0.02
20 3 0.06
21 2 0.04
22 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTTATTTAAAAATA
Found at i:162882 original size:22 final size:22
Alignment explanation
Indices: 162857--162899 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
162847 AATTTAGTAG
*
162857 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
162879 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
162900 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:162922 original size:32 final size:32
Alignment explanation
Indices: 162884--162985 Score: 125
Period size: 32 Copynumber: 3.5 Consensus size: 32
162874 TAAAATATGA
162884 ATTGATTTATTTTAAATAATTTATTAGTATAG
1 ATTGATTTATTTTAAATAATTTATTAGTATAG
162916 ATTGATTTATTTT-AA-AA--TA-T-G----G
1 ATTGATTTATTTTAAATAATTTATTAGTATAG
*
162938 ATTGATTTATTTTAAATAATTTATTAGTATAT
1 ATTGATTTATTTTAAATAATTTATTAGTATAG
162970 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
162986 ATATGGATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
22 14 0.24
23 2 0.03
24 2 0.03
26 3 0.05
27 2 0.03
28 3 0.05
30 2 0.03
31 2 0.03
32 29 0.49
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTGATTTATTTTAAATAATTTATTAGTATAG
Found at i:162922 original size:54 final size:54
Alignment explanation
Indices: 162781--163226 Score: 324
Period size: 54 Copynumber: 8.1 Consensus size: 54
162771 TAATAATTTT
* * * * *
162781 ATTTATTTTAAAATAATTTATTA-TA-A-AATAATTTATTATAAAATATGGATTA
1 ATTTATTTT-AAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
* * *
162833 ATTTATTTAAAAATAATTTAGTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTT-TAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
*
162888 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
* *
162942 ATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
* * * * * * *
162996 ATTTATTATT--GTAGTTGTA-T-GGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATT-TTAAATAATT-TATTAGTATAGATTGA-TTT--AT--TTTA-AAATATGAATTG
* * * *
163054 ATTTATTTTAAATAATTTATTAGTATGGATTGGTTCATTTT--AA-AT-AATTT
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
* * * * * * * *** *
163104 ATTTGTATGGGTTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTTTATGGATTG
1 A-TT-TAT--TTTAAATAATTTAT-TAGTATAGATTGATTTA-T-TT-TA-AAATATGAATTG
163166 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGA-ATTG
163220 ATTTATT
1 ATTTATT
163227 ATTGTAGTTG
Statistics
Matches: 309, Mismatches: 54, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
50 5 0.02
51 4 0.01
52 31 0.10
53 11 0.04
54 139 0.45
55 39 0.13
56 4 0.01
57 10 0.03
58 40 0.13
59 8 0.03
60 10 0.03
61 4 0.01
62 4 0.01
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTG
Found at i:163023 original size:134 final size:134
Alignment explanation
Indices: 162879--163643 Score: 1048
Period size: 134 Copynumber: 5.6 Consensus size: 134
162869 TATTTTAAAA
*
162879 TATGAATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATGGATTGA
*
162943 TTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
65 TTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
163008 AGTTG
130 AGTTG
163013 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTT---TAA---A--A-T
* * * * *
163078 ATGGATTGGTTCATTTTAAATAATTTATTTGTATGGGTTGATTTATTTTAAAATATGGATTGATT
56 ATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATT
*
163143 TATTATTGTAGTTT
121 TATTATTGTAGTTG
*
163157 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAAATATAGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATGGATTGA
* * * * *
163221 TTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
65 TTTATTTTAAATAATTTA-TTAGTATAGATTGATTTATTTT-AA-AA--TA-T-GGATTGATTTA
* **
163279 TTTATTTTAAAAT-
123 -TTATTGT-AGTTG
* * *
163292 T-TGGATTGCTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATTTGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
163356 TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
163421 GTTG
131 GTTG
*
163425 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATTTGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
* *
163490 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
163555 GTTG
131 GTTG
163559 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
163624 TTATTTTAAATAATTTATTA
66 TTATTTTAAATAATTTATTA
163644 TTGTAGTTGT
Statistics
Matches: 562, Mismatches: 38, Indels: 62
0.85 0.06 0.09
Matches are distributed among these distances:
128 21 0.04
129 4 0.01
130 4 0.01
132 6 0.01
133 8 0.01
134 341 0.61
135 13 0.02
136 6 0.01
137 1 0.00
138 7 0.01
139 4 0.01
140 24 0.04
141 1 0.00
143 5 0.01
144 117 0.21
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
GTTG
Found at i:163029 original size:80 final size:81
Alignment explanation
Indices: 162933--163534 Score: 267
Period size: 80 Copynumber: 7.3 Consensus size: 81
162923 TATTTTAAAA
162933 TATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGAT
162998 TTATTATTGTAGTT-G
66 TTATTATTGTAGTTAG
*
163013 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTT-AAATA---ATTTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-ATATTGATTTATTTTAAAATATGGATTGA
*
163073 TTAGTATGGATTG--GTTCA-
65 TT--TAT-TATTGTAGTT-AG
* ** * * ** * ** **
163091 TTTTAAATAATTTATTTGTATGGGTTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
1 TATGGATTGATTTATTT-TA---AATAATTTA--TTAGTATAT--ATTGATTTA-T-TT-TA-AA
* *
163156 TTATGGATTGATTTATTTTAAATAATTTA-TTAG
54 ATATGGATTGATTTA--TT--AT--TGTAGTTAG
* * * ***
163189 TATAGATTGATTTATTTT-AA-AA--TA-TAG-AT-TGATTTA-TTATTGTAGTTGTATGGATTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAT-ATTGATTTATTTTA-AAATATGGATTG
*
163246 ATTTATTTTAAATAATTTA-TTAG
64 ATTTA--TT--AT--TGTAGTTAG
* * ** * * *
163269 TATGGATTGATTTATTTT-AA-AATTTGGATT-GCTTTAT-TTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATTTTAAATAATTT--ATTAG-TATATATTGATTTATTTTA-AAATATGGAT
* *
163330 TGATTTA-T-TT-TA--AAA
62 TGATTTATTATTGTAGTTAG
* * *
163345 TTTGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGAT
163410 TTATTATTGTAGTT-G
66 TTATTATTGTAGTTAG
*
163425 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATTTGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-ATATTGATTTATTTTAAAATATGGATTGA
*
163489 TTTATTTTAAATAATTTA-TTAG
65 TTTA--TT--AT--TGTAGTTAG
163511 TATGGATTGATTTATTTTGAAATA
1 TATGGATTGATTTATTTT-AAATA
163535 TGGATTGATT
Statistics
Matches: 408, Mismatches: 55, Indels: 111
0.71 0.10 0.19
Matches are distributed among these distances:
76 44 0.11
77 18 0.04
78 23 0.06
79 13 0.03
80 170 0.42
81 3 0.01
82 10 0.02
83 5 0.01
84 14 0.03
85 8 0.02
86 55 0.13
87 9 0.02
88 2 0.00
89 1 0.00
90 2 0.00
91 2 0.00
92 3 0.01
94 7 0.02
95 2 0.00
97 3 0.01
98 14 0.03
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (81 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTAG
Found at i:163041 original size:14 final size:14
Alignment explanation
Indices: 163022--163074 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
163012 GTATGGATTG
163022 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
163036 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
163054 ATTTATTTTAAATA
1 ATTTATTTTAAATA
163068 ATTTATT
1 ATTTATT
163075 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:163054 original size:32 final size:32
Alignment explanation
Indices: 163012--163397 Score: 203
Period size: 32 Copynumber: 12.7 Consensus size: 32
163002 TATTGTAGTT
163012 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
163044 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * *
163076 GTATGGATTGGTTCATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* **
163108 GTATGGGTTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * *
163139 G-ATTTATT-ATTGTAGTTTTATGGATTGATTTATT-
1 GTATGGATTGATT-TA-TTTTA---AATAATTTATTA
* * * * *
163173 -T-T-AAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-TA-AATAATTTA--TT--A
* * *
163210 ATATAGATTGATTTA--TT--AT--TGTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
163236 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
163268 GTATGGATTGATTTATTTT--A-AA---A-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
163292 -T-TGGATTGCTTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
163322 GTATGGATTGATTTATTTT--A-AA---A-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
163346 -T-TGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
163376 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
163398 ATATAGATTG
Statistics
Matches: 276, Mismatches: 31, Indels: 94
0.69 0.08 0.23
Matches are distributed among these distances:
22 31 0.11
23 2 0.01
24 2 0.01
25 6 0.02
26 15 0.05
28 4 0.01
29 11 0.04
30 13 0.05
31 13 0.05
32 153 0.55
33 5 0.02
34 10 0.04
35 1 0.00
36 1 0.00
38 1 0.00
39 1 0.00
40 7 0.03
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:163203 original size:18 final size:18
Alignment explanation
Indices: 163180--163227 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
163170 ATTTTAAATA
*
163180 ATTTATTAGTATAGATTG
1 ATTTATTAATATAGATTG
163198 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AATATAGATTG
163220 ATTTATTA
1 ATTTATTA
163228 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATAGATTG
Found at i:163229 original size:224 final size:214
Alignment explanation
Indices: 162933--163360 Score: 694
Period size: 224 Copynumber: 2.0 Consensus size: 214
162923 TATTTTAAAA
* *
162933 TATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
162998 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
* * *
163063 AAATAATTTATTAGTATGGATTGGTTCATTTTAAATAATTTATTTGTATGGGTTGATTTATTTTA
131 --A-AA---A-T--T-TGGATTGCTTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA
163128 AAATATGGATTGATTTATTATTGTAGTTT
186 AAATATGGATTGATTTATTATTGTAGTTT
163157 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
*
163222 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
* *
163287 AAAATTTGGATTGCTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATTTGGAT
131 AAAATTTGGATTGCTTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGAT
163352 TGATTTATT
196 TGATTTATT
163361 TTAAATAATT
Statistics
Matches: 196, Mismatches: 8, Indels: 10
0.92 0.04 0.05
Matches are distributed among these distances:
214 63 0.32
215 1 0.01
217 1 0.01
218 1 0.01
221 2 0.01
222 1 0.01
224 127 0.65
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (214 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAATTTGGATTGCTTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGAT
TGATTTATTATTGTAGTTT
Found at i:163308 original size:54 final size:54
Alignment explanation
Indices: 163239--163643 Score: 338
Period size: 54 Copynumber: 7.5 Consensus size: 54
163229 TGTAGTTGTA
163239 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
*
163293 TGGATTGCTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
* *
163347 TGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
* *
163401 TAGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATT
1 TGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AATT
* * * ** * * * *
163451 T--ATT-AGTATGAATTGATTTATTTTA-AAATTTGGATTGATTTATTTTAAATAATT
1 TGGATTGA-T-TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AATT
* * * * * * * * **
163505 T--ATT-A-GTATGGATTGATTTATTT-TGAAATATGGATTGATTTATTATTGTAGTTGT
1 TGGATTGATTTAT--TTTAAATAATTTAT-TAGTATGGATTGATTTATT-TT-AAAAT-T
* *
163560 ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
1 -TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
163615 TGGATTGATTTATTTTAAATAATTTATTA
1 TGGATTGATTTATTTTAAATAATTTATTA
163644 TTGTAGTTGT
Statistics
Matches: 286, Mismatches: 41, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
47 1 0.00
48 25 0.09
49 6 0.02
50 6 0.02
51 2 0.01
52 2 0.01
53 7 0.02
54 193 0.67
55 7 0.02
56 3 0.01
57 2 0.01
58 27 0.09
59 2 0.01
60 3 0.01
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATT
Found at i:163391 original size:18 final size:18
Alignment explanation
Indices: 163368--163415 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
163358 ATTTTAAATA
*
163368 ATTTATTAGTATAGATTG
1 ATTTATTAATATAGATTG
163386 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AATATAGATTG
163408 ATTTATTA
1 ATTTATTA
163416 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATAGATTG
Found at i:163406 original size:188 final size:188
Alignment explanation
Indices: 163157--163548 Score: 748
Period size: 188 Copynumber: 2.1 Consensus size: 188
163147 ATTGTAGTTT
163157 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
*
163222 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
*
163287 AAAATTTGGATTGCTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
131 AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
163345 TTTGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
163410 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
*
163475 AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAA
131 AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
163533 TATGGATTGATTTATT
1 TATGGATTGATTTATT
163549 ATTGTAGTTG
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
188 199 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (188 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:163466 original size:32 final size:32
Alignment explanation
Indices: 163424--163534 Score: 134
Period size: 32 Copynumber: 3.8 Consensus size: 32
163414 TATTGTAGTT
163424 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
163456 GTATGAATTGATTTATTTT--A-AA---A-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
163480 -T-TGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
163510 GTATGGATTGATTTATTTTGAAATA
1 GTATGGATTGATTTATTTT-AAATA
163535 TGGATTGATT
Statistics
Matches: 66, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
22 15 0.23
23 1 0.02
24 1 0.02
25 3 0.05
26 1 0.02
28 1 0.02
29 3 0.05
30 1 0.02
31 1 0.02
32 34 0.52
33 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:163525 original size:18 final size:18
Alignment explanation
Indices: 163502--163549 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
163492 ATTTTAAATA
*
163502 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
163520 ATTTATTTTGAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
163542 ATTTATTA
1 ATTTATTA
163550 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:163536 original size:22 final size:22
Alignment explanation
Indices: 163511--163581 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 22
163501 AATTTATTAG
163511 TATGGATTGATTTATTTTGAAA
1 TATGGATTGATTTATTTTGAAA
**
163533 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATT-TTG-A--AA
163559 TATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTGAAA
163580 TA
1 TA
163582 ATTTATTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 2 0.05
22 16 0.39
23 4 0.10
24 1 0.02
25 2 0.05
26 16 0.39
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTGAAA
Found at i:163567 original size:80 final size:80
Alignment explanation
Indices: 163481--163628 Score: 278
Period size: 80 Copynumber: 1.9 Consensus size: 80
163471 TTTTAAAATT
* *
163481 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTGATTT
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTT
163546 ATTATTGTAGTTGTA
66 ATTATTGTAGTTGTA
163561 TGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTT
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTT
163626 ATT
66 ATT
163629 TTAAATAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (80 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTT
ATTATTGTAGTTGTA
Found at i:163616 original size:22 final size:22
Alignment explanation
Indices: 163591--163633 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
163581 AATTTATTAG
163591 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
163613 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
163634 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:163619 original size:188 final size:185
Alignment explanation
Indices: 163157--163643 Score: 653
Period size: 188 Copynumber: 2.6 Consensus size: 185
163147 ATTGTAGTTT
*
163157 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTA-TTT-AAT-ATGTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
* *** *
163222 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
63 TGATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
*
163287 AAAATTTGGATTGCTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
128 AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
163345 TTTGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTA-TTT-AAT-ATGTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
* ***
163410 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
63 TGATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
*
163475 AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAA
128 AAAATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
163533 TATGGATTGATTTA-TT-AT-TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAG-TA
1 TATGGATTGATTTATTTAATATGTA-TTAGTATAGATTGATTTATTTT-AA-AA--TA-TAGAT-
*
163593 TGAATTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTA
59 TG-ATTGA-TTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTA
163644 TTGTAGTTGT
Statistics
Matches: 278, Mismatches: 12, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
182 21 0.08
183 4 0.01
184 4 0.01
186 5 0.02
187 5 0.02
188 232 0.83
189 7 0.03
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (185 bp):
TATGGATTGATTTATTTAATATGTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTGA
TTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
ATTTGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:164117 original size:2 final size:2
Alignment explanation
Indices: 164110--164166 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
164100 CATTCTTTCA
164110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
164152 AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT A
164167 ATTATGATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:169802 original size:6 final size:6
Alignment explanation
Indices: 169791--169830 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
169781 TTCTGACAAA
* * *
169791 AGAATC AGAATC AGAATC AGAAGC AGAAGC AGAAGC AGAA
1 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC AGAA
169831 CAAGCAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.53, C:0.15, G:0.25, T:0.07
Consensus pattern (6 bp):
AGAAGC
Found at i:169808 original size:12 final size:12
Alignment explanation
Indices: 169791--169830 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
169781 TTCTGACAAA
*
169791 AGAATCAGAATC
1 AGAATCAGAAGC
169803 AGAATCAGAAGC
1 AGAATCAGAAGC
*
169815 AGAAGCAGAAGC
1 AGAATCAGAAGC
169827 AGAA
1 AGAA
169831 CAAGCAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.53, C:0.15, G:0.25, T:0.07
Consensus pattern (12 bp):
AGAATCAGAAGC
Found at i:179654 original size:32 final size:33
Alignment explanation
Indices: 179613--179678 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
179603 TACAGTTCAA
179613 ACCAGCGCAA-CACCATTAATGTCCCTTATCAC
1 ACCAGCGCAAGCACCATTAATGTCCCTTATCAC
179645 ACCAGCGCAAGCACCATTAATGTCCCTTATCAC
1 ACCAGCGCAAGCACCATTAATGTCCCTTATCAC
179678 A
1 A
179679 TAATATAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.32, C:0.36, G:0.11, T:0.21
Consensus pattern (33 bp):
ACCAGCGCAAGCACCATTAATGTCCCTTATCAC
Found at i:188317 original size:18 final size:18
Alignment explanation
Indices: 188272--188321 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 18
188262 ATTTGGATAA
188272 GTATAGATTGATTTATTT
1 GTATAGATTGATTTATTT
*
188290 -TA-A-A-TAATTTATTT
1 GTATAGATTGATTTATTT
188304 GTATAGATTGATTTATTT
1 GTATAGATTGATTTATTT
188322 TAAAATATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 9 0.35
15 3 0.12
16 2 0.08
17 3 0.12
18 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (18 bp):
GTATAGATTGATTTATTT
Found at i:188373 original size:80 final size:80
Alignment explanation
Indices: 188272--188495 Score: 350
Period size: 80 Copynumber: 2.8 Consensus size: 80
188262 ATTTGGATAA
*
188272 GTATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGA
1 GTAT-GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGA
188337 TT-TATT-ATTGTAGTT
65 TTGT-TTGATTGTAGTT
* *
188352 GTATGGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATAT-G-TTTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGA
188415 TTGTTTGATTGTAGTT
65 TTGTTTGATTGTAGTT
*
188431 GTATGATTGATTTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 GTATGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
188495 T
66 T
188496 ATTTTAAATA
Statistics
Matches: 133, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
77 40 0.30
78 18 0.14
79 20 0.15
80 55 0.41
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (80 bp):
GTATGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
TGTTTGATTGTAGTT
Found at i:188499 original size:21 final size:22
Alignment explanation
Indices: 188462--188503 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
188452 AATTTATTAG
188462 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
188484 TATGGATTGA-TTATTTTAAA
1 TATGGATTGATTTATTTTAAA
188504 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:188627 original size:15 final size:15
Alignment explanation
Indices: 188607--188635 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
188597 TAAAAAATCA
188607 GTTTATTTATATTTC
1 GTTTATTTATATTTC
188622 GTTTATTTATATTT
1 GTTTATTTATATTT
188636 TAATTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (15 bp):
GTTTATTTATATTTC
Found at i:189119 original size:19 final size:19
Alignment explanation
Indices: 189095--189131 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
189085 TTGTAATGTC
189095 AATTAAAATAATA-TAAATT
1 AATTAAAA-AATATTAAATT
189114 AATTAAAAAATATTAAAT
1 AATTAAAAAATATTAAAT
189132 CATTTTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAAAAAATATTAAATT
Found at i:190733 original size:20 final size:18
Alignment explanation
Indices: 190691--190758 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
190681 ATATTTATCT
*
190691 CGAATGACCACTATGTCC
1 CGAAGGACCACTATGTCC
*
190709 CGAAGGACCACTTATTGTTC
1 CGAAGGACCAC-TA-TGTCC
* *
190729 CGAAGAACCACCATGTCC
1 CGAAGGACCACTATGTCC
190747 CGAAGGACCACT
1 CGAAGGACCACT
190759 TAGACCCTCG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 24 0.59
19 3 0.07
20 14 0.34
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
CGAAGGACCACTATGTCC
Found at i:192678 original size:13 final size:13
Alignment explanation
Indices: 192660--192684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
192650 ACGGGAGGAG
192660 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
192673 AGGAAGAAGAAG
1 AGGAAGAAGAAG
192685 TTCTGGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:193830 original size:83 final size:82
Alignment explanation
Indices: 193743--193971 Score: 259
Period size: 82 Copynumber: 2.8 Consensus size: 82
193733 GCCGCAATTA
* *
193743 AGTGGTAATTTCGCGGCGTTTATAGCTA-AAACGCCGCAATAGAT-ATGTTTATAGTGGCGTTTT
1 AGTGGTAATTTAGCGGCGTTTATA-C-ACAAACGCCGCAATAG-TGATGTTTATAGTGGCGTTTG
*
193806 TTCAACAAACATCG-TAATAG
63 TTCAACAAACAACGCT-ATAG
* * *
193826 AGTGGTAATTTAGCGGTGTTTTTACACAAACGCCGCAATAGTGTTGTTTATAGTGGCGTTTGTTC
1 AGTGGTAATTTAGCGGCGTTTATACACAAACGCCGCAATAGTGATGTTTATAGTGGCGTTTGTTC
*
193891 AATAAACAACGCTATAG
66 AACAAACAACGCTATAG
** * * * *
193908 AGAAGTAATTTAGCGGCGTTTATCAAACAAACACCGCAATA-TTATTGTTTATAGTGGCATTTGT
1 AGTGGTAATTTAGCGGCGTTTAT-ACACAAACGCCGCAATAGTGA-TGTTTATAGTGGCGTTTGT
193972 GCAAAAAATG
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
81 2 0.02
82 68 0.54
83 55 0.44
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (82 bp):
AGTGGTAATTTAGCGGCGTTTATACACAAACGCCGCAATAGTGATGTTTATAGTGGCGTTTGTTC
AACAAACAACGCTATAG
Found at i:193866 original size:41 final size:42
Alignment explanation
Indices: 193709--193948 Score: 133
Period size: 41 Copynumber: 5.8 Consensus size: 42
193699 AAAATGTTAC
*
193709 TTTAGCGGCATTTTTTA-AACAAACGCCGCAATTA-AGTGGTAA
1 TTTAGCGGC-GTTTTTACAACAAACGCCGCAA-TAGAGTGGTAA
* * * *
193751 TTTCGCGGCGTTTATAGCTA-AAACGCCGCAATAGA-TATGT--
1 TTTAGCGGCGTTTTTA-CAACAAACGCCGCAATAGAGT-GGTAA
* * ** *
193791 TTATAGTGGCGTTTTTTCAACAAACATCGTAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTACAACAAACGCCGCAATAGAGTGGTAA
* * *
193834 TTTAGCGGTGTTTTTAC-ACAAACGCCGCAATAGTGTTGT--
1 TTTAGCGGCGTTTTTACAACAAACGCCGCAATAGAGTGGTAA
* * ** * **
193873 TTATAGTGGCGTTTGTT-CAATAAACAACGCTATAGAGAAGTAA
1 TT-TAGCGGCGTTT-TTACAACAAACGCCGCAATAGAGTGGTAA
* *
193916 TTTAGCGGCGTTTAT-CAAACAAACACCGCAATA
1 TTTAGCGGCGTTTTTAC-AACAAACGCCGCAATA
193949 TTATTGTTTA
Statistics
Matches: 147, Mismatches: 36, Indels: 30
0.69 0.17 0.14
Matches are distributed among these distances:
39 2 0.01
40 14 0.10
41 68 0.46
42 58 0.39
43 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTACAACAAACGCCGCAATAGAGTGGTAA
Found at i:193991 original size:83 final size:80
Alignment explanation
Indices: 193771--194068 Score: 228
Period size: 83 Copynumber: 3.6 Consensus size: 80
193761 TTTATAGCTA
* * * **
193771 AAACGCCGCAATA-GATATGTTTATAGTGGCGTTTTTTCAACAAACAT--CGTAATAGAGTGGTA
1 AAACGCCGCAATATG-T-TGTTTATAGTGGC-ATTTGTCAA-AAA-ATGCCGCAATAGAGAAGTA
* * *
193833 ATTTAGCGGTGTTTTTACAC
61 ATTTAGCGGCGTTTTCAAAC
* * *** *
193853 AAACGCCGCAATAGTGTTGTTTATAGTGGCGTTTGTTCAATAAACAACGCTATAGAGAAGTAATT
1 AAACGCCGCAATA-TGTTGTTTATAGTGGCATTTG-TCAAAAAATGCCGCAATAGAGAAGTAATT
193918 TAGCGGCGTTTATCAAAC
64 TAGCGGCGTTT-TCAAAC
* *
193936 AAACACCGCAATATTATTGTTTATAGTGGCATTTGTGCAAAAAATGCCGCAATAGAGTAA-TAAT
1 AAACGCCGCAATA-TGTTGTTTATAGTGGCATTTGT-CAAAAAATGCCGCAATAGAG-AAGTAAT
* * * **
194000 ATAGCGACATTTGTCCTAC
63 TTAGCGGCGTTT-TCAAAC
* * *
194019 AAACGCCGTAATATGTTGTTTATCGTGGCATTTAT-ATAAAAATGCCGCAA
1 AAACGCCGCAATATGTTGTTTATAGTGGCATTTGTCA-AAAAATGCCGCAA
194069 AAATAAGCAC
Statistics
Matches: 176, Mismatches: 31, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
80 2 0.01
81 18 0.10
82 74 0.42
83 79 0.45
84 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (80 bp):
AAACGCCGCAATATGTTGTTTATAGTGGCATTTGTCAAAAAATGCCGCAATAGAGAAGTAATTTA
GCGGCGTTTTCAAAC
Found at i:197732 original size:2 final size:2
Alignment explanation
Indices: 197725--197758 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
197715 AGATACTACA
197725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
197759 TGTAGAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:198740 original size:43 final size:42
Alignment explanation
Indices: 198660--198740 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 42
198650 TTTCGCATAG
**
198660 TTAGCGGCGTTTGTATCAGAAAACGCCGCTATGTACCAACTT
1 TTAGCGGCGTTTGTATCAGAAAACGCCGCTACATACCAACTT
198702 TTAGCGGCGTTTGTATACTA-AAAACGCCGCTACATACCA
1 TTAGCGGCGTTTGTAT-C-AGAAAACGCCGCTACATACCA
198741 GGAATATAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 16 0.46
43 18 0.51
44 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (42 bp):
TTAGCGGCGTTTGTATCAGAAAACGCCGCTACATACCAACTT
Found at i:198925 original size:43 final size:43
Alignment explanation
Indices: 198865--198992 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 43
198855 AAATGTCGCG
* * * *
198865 AAATATCAACACTTATTGCGGCATTTGTGGTAAAAACGCCACT
1 AAATATCGACACCTATTGCGGCGTTTTTGGTAAAAACGCCACT
* * * *
198908 AAATATTGACACCTATTGCGGCGTTTTTAAG-ACAAACGCCGCT
1 AAATATCGACACCTATTGCGGCGTTTTT-GGTAAAAACGCCACT
**
198951 AAATATCGGTACCTATTGCGGCGTTTTTGGTTAACAAACGCC
1 AAATATCGACACCTATTGCGGCGTTTTTGG-TAA-AAACGCC
198993 GTAAACTTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 58 0.85
44 2 0.03
45 7 0.10
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (43 bp):
AAATATCGACACCTATTGCGGCGTTTTTGGTAAAAACGCCACT
Found at i:199128 original size:107 final size:107
Alignment explanation
Indices: 198941--199145 Score: 302
Period size: 107 Copynumber: 1.9 Consensus size: 107
198931 TTTTTAAGAC
* *
198941 AAACGCCGCTAAATATCGGTACCTATTGCGGCGTTTTTGGTTAACAAACGCCGTAAACTTTAGCG
1 AAACGCCGCTAAATATCGGTACCTATTACGGCGTTTTTAGTTAACAAACGCCGTAAACTTTAGCG
*
199006 GTGCTATTTTCAGCGGCGCATTTTACGGCGTTTGTTAACCAA
66 GCGCTATTTTCAGCGGCGCATTTTACGGCGTTTGTTAACCAA
* * * * *
199048 AAACGTCGCTATATATCGTTACCTATTACGGTGTTTTTAGTTAACAAACGTCGTAAACTTTAGCG
1 AAACGCCGCTAAATATCGGTACCTATTACGGCGTTTTTAGTTAACAAACGCCGTAAACTTTAGCG
* * * *
199113 GCGCTATTTTTAGCGGCGTATTTTGCGGTGTTT
66 GCGCTATTTTCAGCGGCGCATTTTACGGCGTTT
199146 TCCATAACGC
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
107 86 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (107 bp):
AAACGCCGCTAAATATCGGTACCTATTACGGCGTTTTTAGTTAACAAACGCCGTAAACTTTAGCG
GCGCTATTTTCAGCGGCGCATTTTACGGCGTTTGTTAACCAA
Found at i:199136 original size:14 final size:15
Alignment explanation
Indices: 199106--199136 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
199096 CGTCGTAAAC
199106 TTTAGCGGCGCTATT
1 TTTAGCGGCGCTATT
199121 TTTAGCGGCG-TATT
1 TTTAGCGGCGCTATT
199135 TT
1 TT
199137 GCGGTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (15 bp):
TTTAGCGGCGCTATT
Found at i:202213 original size:29 final size:29
Alignment explanation
Indices: 202181--202264 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
202171 GATCTTAAAT
202181 TTATTTAATATTTTATATTAATCCTCAAA
1 TTATTTAATATTTTATATTAATCCTCAAA
* * *
202210 TTATTT--TA----A-ATTGATCTTCAAT
1 TTATTTAATATTTTATATTAATCCTCAAA
*
202232 TTCTTTAATATTTTATATTAATCCTCAAA
1 TTATTTAATATTTTATATTAATCCTCAAA
202261 TTAT
1 TTAT
202265 GATTTTATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
22 15 0.38
23 1 0.03
24 2 0.05
27 2 0.05
28 1 0.03
29 19 0.47
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.54
Consensus pattern (29 bp):
TTATTTAATATTTTATATTAATCCTCAAA
Found at i:202225 original size:51 final size:51
Alignment explanation
Indices: 202163--202264 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
202153 AAAGACCTCA
202163 TTTAAACTGATCTTAAATTTATTTAATATTTTATATTAATCCTCAAATTAT
1 TTTAAACTGATCTTAAATTTATTTAATATTTTATATTAATCCTCAAATTAT
* * *
202214 TTTAAATTGATCTTCAATTTCTTTAATATTTTATATTAATCCTCAAATTAT
1 TTTAAACTGATCTTAAATTTATTTAATATTTTATATTAATCCTCAAATTAT
202265 GATTTTATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (51 bp):
TTTAAACTGATCTTAAATTTATTTAATATTTTATATTAATCCTCAAATTAT
Found at i:202230 original size:22 final size:22
Alignment explanation
Indices: 202189--202230 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
202179 ATTTATTTAA
*
202189 TATTTTATATTAATCCTCAAAT
1 TATTTTAAATTAATCCTCAAAT
* *
202211 TATTTTAAATTGATCTTCAA
1 TATTTTAAATTAATCCTCAA
202231 TTTCTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTTTAAATTAATCCTCAAAT
Found at i:202627 original size:18 final size:20
Alignment explanation
Indices: 202604--202652 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
202594 ATAAAATGTT
202604 TTTAAAATTAAAGA-C-TAA
1 TTTAAAATTAAAGATCATAA
*
202622 TTTAAAA-TAAATATCATAA
1 TTTAAAATTAAAGATCATAA
202641 TTTAAAAATTAA
1 TTT-AAAATTAA
202653 TATAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.19
18 8 0.31
19 6 0.23
20 4 0.15
21 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TTTAAAATTAAAGATCATAA
Found at i:202654 original size:20 final size:20
Alignment explanation
Indices: 202567--202687 Score: 70
Period size: 20 Copynumber: 6.1 Consensus size: 20
202557 TAATCAAATG
202567 AAATT-ATACTAATAATTTAA
1 AAATTAATA-TAATAATTTAA
* * ** *
202587 AATTTATATAAAATGTTTTTA
1 AAATTA-ATATAATAATTTAA
* *
202608 AAATTAA-AGACTAATTT-A
1 AAATTAATATAATAATTTAA
* *
202626 AAATAAATATCATAATTTAA
1 AAATTAATATAATAATTTAA
* * *
202646 AAATTAATATAAAAATATATT
1 AAATTAATATAATAATTTA-A
*
202667 AAATT-TTATAATAATTTAA
1 AAATTAATATAATAATTTAA
202686 AA
1 AA
202688 TGAAAATCAC
Statistics
Matches: 73, Mismatches: 23, Indels: 11
0.68 0.21 0.10
Matches are distributed among these distances:
18 7 0.10
19 15 0.21
20 31 0.42
21 17 0.23
22 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATTAATATAATAATTTAA
Found at i:205868 original size:21 final size:21
Alignment explanation
Indices: 205842--205882 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
205832 AAAGGGAAAA
205842 AATAAAATAACAT-AAAAAAGT
1 AATAAAATAA-ATGAAAAAAGT
205863 AATAAAATAAATGAAAAAAG
1 AATAAAATAAATGAAAAAAG
205883 GAACCTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (21 bp):
AATAAAATAAATGAAAAAAGT
Found at i:207120 original size:3 final size:3
Alignment explanation
Indices: 207096--207141 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
207086 GCCTACAAAG
207096 ATA A-A ATA AT- ATA TATA TATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
207141 A
1 A
207142 ATAAATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 29 0.73
4 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:207152 original size:15 final size:13
Alignment explanation
Indices: 207099--207166 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 13
207089 TACAAAGATA
207099 AAATAATATATATAT
1 AAATAATA-ATA-AT
207114 ATAATAATAATAAT
1 A-AATAATAATAAT
207128 -AATAATAATAAT
1 AAATAATAATAAT
207140 AAATAAATAAATAAAT
1 AAAT-AAT-AAT-AAT
*
207156 AAACAATAATA
1 AAATAATAATA
207167 TATTTTTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
12 12 0.26
13 4 0.09
14 8 0.17
15 10 0.21
16 13 0.28
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:210596 original size:21 final size:20
Alignment explanation
Indices: 210550--210588 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
210540 TAGCAAACCT
*
210550 TAAATTCCAAATCTTAAACA
1 TAAATTCCAAACCTTAAACA
*
210570 TGAAATTCTAAACCTTAAA
1 T-AAATTCCAAACCTTAAA
210589 TTATAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.06
21 15 0.94
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (20 bp):
TAAATTCCAAACCTTAAACA
Found at i:214091 original size:42 final size:42
Alignment explanation
Indices: 214039--214131 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
214029 ACTTAGTAAG
* * *
214039 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTAGAGCATGATGATTAAA
*
214081 TCCTTAGGGCCATCAGTAAGTCTTTAGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTAGAGCATGATGATTAAA
*
214123 TTCTTAGGG
1 TCCTTAGGG
214132 TAATTGTAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (42 bp):
TCCTTAGGGCCATCAATAAGTCTTTAGAGCATGATGATTAAA
Found at i:214211 original size:92 final size:93
Alignment explanation
Indices: 214089--214260 Score: 283
Period size: 92 Copynumber: 1.9 Consensus size: 93
214079 AATCCTTAGG
* * * *
214089 GCCATCAGTAAGTCTTTAGAGCATGATGATTAAATTCTTAGGGTAA-TTGTAAGCCTTCACGGAA
1 GCCATCAATAAGTCTTTAGAGCAAGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAA
214153 GAGTAGTGAAGCAAACCCATCAGTATGT
66 GAGTAGTGAAGCAAACCCATCAGTATGT
* *
214181 GCCATCAATAAGTCTTTCGAGCAAGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAATAAGTCTTTAGAGCAAGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAA
214246 GAGTAGTGAAGCAAA
66 GAGTAGTGAAGCAAA
214261 TTATCAGTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 41 0.56
93 32 0.44
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (93 bp):
GCCATCAATAAGTCTTTAGAGCAAGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAA
GAGTAGTGAAGCAAACCCATCAGTATGT
Found at i:214787 original size:53 final size:53
Alignment explanation
Indices: 214724--215038 Score: 409
Period size: 53 Copynumber: 5.9 Consensus size: 53
214714 AAAATCACAC
*
214724 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * *
214777 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
214830 CAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * **
214882 CAGAAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACATGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * * * ***
214935 CAGAAGATTATTTGAGTTCTACTCCCTGAAGCAATAGGGACCGAACCCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * * *
214988 TAGAAGATTGTTCGAGTTCCTTAATCCCTTAA-CAAGAGGGAACAAACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
215039 CATTTGAAGA
Statistics
Matches: 232, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
52 48 0.21
53 159 0.69
54 16 0.07
55 9 0.04
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:214914 original size:105 final size:106
Alignment explanation
Indices: 214724--214982 Score: 403
Period size: 105 Copynumber: 2.5 Consensus size: 106
214714 AAAATCACAC
* *
214724 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATT
* * * *
214789 CGAGTTCTACTCCCTAAAGCAAGAGGGAGTGAACCCGTAGG
66 CGAGTTCTACCCCCTAAAGCAAGAGGGAGCGAACACGTAAG
214830 CAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATT
* *
214894 CGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACATGTAAG
66 CGAGTTCTACCCCCTAAAGCAAGAGGGAGCGAACACGTAAG
* * * *
214935 CAGAAGATTATTTGAGTTCTACTCCCTGAAGCAATAGGGACCGAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
214983 ATTTTTAGAA
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
105 95 0.68
106 45 0.32
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (106 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATT
CGAGTTCTACCCCCTAAAGCAAGAGGGAGCGAACACGTAAG
Found at i:215432 original size:24 final size:23
Alignment explanation
Indices: 215403--215475 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
215393 GTTCTAGAGT
*
215403 AAAAAAGGAGGGGACCAGACATAG
1 AAAAAA-GAGGGAACCAGACATAG
* * * *
215427 AAAAAAAAGAGCA-CAGA-GT--
1 AAAAAAGAGGGAACCAGACATAG
215446 AAAAAAGAGGGAACCAGACATAG
1 AAAAAAGAGGGAACCAGACATAG
215469 AAAAAAG
1 AAAAAAG
215476 GAGAGCACAG
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
19 10 0.27
20 4 0.11
21 2 0.05
22 4 0.11
23 11 0.30
24 6 0.16
ACGTcount: A:0.59, C:0.11, G:0.26, T:0.04
Consensus pattern (23 bp):
AAAAAAGAGGGAACCAGACATAG
Found at i:215462 original size:42 final size:44
Alignment explanation
Indices: 215398--215493 Score: 160
Period size: 43 Copynumber: 2.2 Consensus size: 44
215388 GGGCAGTTCT
*
215398 AGAGTAAAAAAGGAGGGGACCAGACATAGAAAAAA-AAGAGCAC
1 AGAGTAAAAAAGGAGGGAACCAGACATAGAAAAAAGAAGAGCAC
*
215441 AGAGTAAAAAA-GAGGGAACCAGACATAGAAAAAAGGAGAGCAC
1 AGAGTAAAAAAGGAGGGAACCAGACATAGAAAAAAGAAGAGCAC
215484 AGAGTAAAAA
1 AGAGTAAAAA
215494 CGGGAGAGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 22 0.44
43 28 0.56
ACGTcount: A:0.57, C:0.10, G:0.27, T:0.05
Consensus pattern (44 bp):
AGAGTAAAAAAGGAGGGAACCAGACATAGAAAAAAGAAGAGCAC
Found at i:219467 original size:22 final size:23
Alignment explanation
Indices: 219442--219497 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
219432 TGTTATATTT
219442 TTATAAAAATTATA-TGA-AATAA
1 TTATAAAAATTATATTGATAAT-A
* *
219464 TTATAGAAAAGTATATTTATAATA
1 TTATA-AAAATTATATTGATAATA
219488 TTATAAAAAT
1 TTATAAAAAT
219498 ACTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 8 0.29
25 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
TTATAAAAATTATATTGATAATA
Found at i:219722 original size:23 final size:23
Alignment explanation
Indices: 219663--219731 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
219653 AGATAATTTA
* *
219663 AAATAATCTTATTTCAAATAAAT
1 AAATAATATTATTTTAAATAAAT
* *
219686 AATTAAAATTATTTTAAATAAAT
1 AAATAATATTATTTTAAATAAAT
*
219709 AAATAATATGATTTTAAA-AAAT
1 AAATAATATTATTTTAAATAAAT
219731 A
1 A
219732 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 5 0.13
23 34 0.87
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (23 bp):
AAATAATATTATTTTAAATAAAT
Found at i:220493 original size:20 final size:20
Alignment explanation
Indices: 220470--220517 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
220460 ATTCATCTAG
*
220470 TATCGATATTGTTCATATAA
1 TATCGATATTGTTCATACAA
220490 TATCGATATTGTTCATACAA
1 TATCGATATTGTTCATACAA
220510 TATCGATA
1 TATCGATA
220518 CTCGAACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATATTGTTCATACAA
Found at i:221699 original size:21 final size:21
Alignment explanation
Indices: 221676--221715 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
221666 ATACTGACAA
*
221676 AAAATAGAAAAA-TGACATGG
1 AAAATAAAAAAATTGACATGG
221696 AAAATAAAAAAATTGACATG
1 AAAATAAAAAAATTGACATG
221716 ACATGTCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAATAAAAAAATTGACATGG
Found at i:223822 original size:14 final size:15
Alignment explanation
Indices: 223794--223829 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
223784 AATTTTCTTC
*
223794 TATTTATTAATTTTT
1 TATTTATTAAATTTT
223809 TATTT-TTAAATTTT
1 TATTTATTAAATTTT
223823 TATTTAT
1 TATTTAT
223830 ATTTATCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTATTAAATTTT
Found at i:223845 original size:27 final size:27
Alignment explanation
Indices: 223815--223901 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
223805 TTTTTATTTT
*
223815 TAAATTTTTATTTATATTTATCTCATA
1 TAAAATTTTATTTATATTTATCTCATA
** *
223842 TAAAAAATTATGTTATTATATATACTC-T-
1 TAAAATTTTAT-TTA-TATTTAT-CTCATA
223870 TAAAATTTTATTTATATTTATCTCATA
1 TAAAATTTTATTTATATTTATCTCATA
223897 TAAAA
1 TAAAA
223902 ATATATTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.06
26 7 0.15
27 16 0.33
28 12 0.25
29 7 0.15
30 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (27 bp):
TAAAATTTTATTTATATTTATCTCATA
Found at i:223903 original size:28 final size:28
Alignment explanation
Indices: 223820--223903 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
223810 ATTTTTAAAT
223820 TTTTATTTATATTTATCTCATATAAAAA
1 TTTTATTTATATTTATCTCATATAAAAA
* *
223848 -ATTATGTTATTATATATACTC-T-T-AAAA
1 TTTTAT-TTA-TATTTAT-CTCATATAAAAA
223875 TTTTATTTATATTTATCTCATATAAAAA
1 TTTTATTTATATTTATCTCATATAAAAA
223903 T
1 T
223904 ATATTGAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
25 3 0.07
26 7 0.16
27 12 0.27
28 13 0.29
29 7 0.16
30 3 0.07
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (28 bp):
TTTTATTTATATTTATCTCATATAAAAA
Found at i:226698 original size:21 final size:21
Alignment explanation
Indices: 226656--226698 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
226646 TTTCTGGGCT
* *
226656 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
226677 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
226698 A
1 A
226699 CGAATATGAA
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:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:227446 original size:23 final size:23
Alignment explanation
Indices: 227402--227446 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
227392 ATTATTATAT
*
227402 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
227425 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
227447 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:229189 original size:17 final size:18
Alignment explanation
Indices: 229164--229197 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
229154 GCTCCCCGAT
229164 ATATATTTTAA-ATTTTG
1 ATATATTTTAATATTTTG
*
229181 ATATTTTTTAATATTTT
1 ATATATTTTAATATTTT
229198 CTGTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATATATTTTAATATTTTG
Found at i:235332 original size:10 final size:10
Alignment explanation
Indices: 235303--235337 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
235293 CAATGTTACT
235303 AGAAAGAGAA
1 AGAAAGAGAA
235313 A-AAAGAAGAA
1 AGAAAG-AGAA
235323 AGAAAGAGAA
1 AGAAAGAGAA
235333 AGAAA
1 AGAAA
235338 CCATGTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AGAAAGAGAA
Found at i:238082 original size:42 final size:42
Alignment explanation
Indices: 238023--238105 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
238013 AAGAGCTGTA
238023 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGAT
1 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGAT
238065 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGA
1 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGA
238106 CGATGAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (42 bp):
GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGAT
Found at i:255449 original size:29 final size:29
Alignment explanation
Indices: 255417--255521 Score: 72
Period size: 29 Copynumber: 3.6 Consensus size: 29
255407 AAATATTTAA
*
255417 AATATAATAATTATTAATTCTAATAATAT
1 AATATAATAATTATTAATTATAATAATAT
* * *
255446 AATATTATATTTTTTAGCATTATAATAATAT
1 AATATAATAATTATTA--ATTATAATAATAT
* * * * *
255477 AAGATATTTTATT-TTTATTTTAATAATAT
1 AATATA-ATAATTATTAATTATAATAATAT
*
255506 -ATA-AAAAATTATTAAT
1 AATATAATAATTATTAAT
255522 AAATTTTTTA
Statistics
Matches: 56, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
26 3 0.05
27 5 0.09
28 2 0.04
29 25 0.45
31 18 0.32
32 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
AATATAATAATTATTAATTATAATAATAT
Found at i:257555 original size:2 final size:2
Alignment explanation
Indices: 257548--257574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
257538 TTCTGAATTT
257548 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
257575 TGTACTTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258074 original size:17 final size:18
Alignment explanation
Indices: 258041--258074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
258031 TCAATTCTGT
*
258041 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
258059 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
258075 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:263200 original size:17 final size:18
Alignment explanation
Indices: 263167--263200 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
263157 TCAATTCTGT
*
263167 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
263185 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
263201 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:265837 original size:14 final size:15
Alignment explanation
Indices: 265804--265836 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
265794 CAAACACCGT
265804 AAAATGTTTTTCAAA
1 AAAATGTTTTTCAAA
*
265819 AAAATGTTTTCCAAA
1 AAAATGTTTTTCAAA
265834 AAA
1 AAA
265837 TATAATCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAATGTTTTTCAAA
Found at i:267774 original size:16 final size:18
Alignment explanation
Indices: 267735--267775 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
267725 TAATTTACTT
267735 AATTTATTATATTAATAA
1 AATTTATTATATTAATAA
*
267753 AGATTTA-TATTTTAA-AA
1 A-ATTTATTATATTAATAA
267770 AATTTA
1 AATTTA
267776 CAACTAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 3 0.14
18 8 0.38
19 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTTATTATATTAATAA
Found at i:268624 original size:15 final size:15
Alignment explanation
Indices: 268601--268630 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
268591 TTATAATATA
268601 AATTATAAAAAAAAT
1 AATTATAAAAAAAAT
*
268616 AATTTTAAAAAAAAT
1 AATTATAAAAAAAAT
268631 TTGAACTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTATAAAAAAAAT
Found at i:271879 original size:14 final size:14
Alignment explanation
Indices: 271862--271894 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
271852 ATTTCTATGT
*
271862 AGGGAATTATTTGC
1 AGGGAATTATTTAC
271876 AGGGAATTATTTAC
1 AGGGAATTATTTAC
271890 AGGGA
1 AGGGA
271895 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:276360 original size:3 final size:3
Alignment explanation
Indices: 276339--276429 Score: 107
Period size: 3 Copynumber: 30.7 Consensus size: 3
276329 GGGATATAAA
* * *
276339 TAT TA- TAT TAT AAT AAT TAT TAT TAT TAT TAT TA- TAT TA- TAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
276384 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAA TATT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT TA
276430 CAACTATTTG
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.08
3 66 0.86
4 5 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:276392 original size:34 final size:35
Alignment explanation
Indices: 276338--276414 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
276328 CGGGATATAA
*
276338 ATATTATATTATAATAATTATTATTATTA-TTATT
1 ATATTATATGATAATAATTATTATTATTATTTATT
* *
276372 ATATTATATGATTATTATTATTATTATTATTTATT
1 ATATTATATGATAATAATTATTATTATTATTTATT
276407 ATTATTAT
1 A-TATTAT
276415 TATTAATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 26 0.68
35 6 0.16
36 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (35 bp):
ATATTATATGATAATAATTATTATTATTATTTATT
Found at i:276418 original size:22 final size:22
Alignment explanation
Indices: 276339--276429 Score: 116
Period size: 22 Copynumber: 4.2 Consensus size: 22
276329 GGGATATAAA
* *
276339 TATTA-TATTATAATAATTA-T
1 TATTATTATTATTATTATTATT
276359 TATTATTATTATTA-TATTATAT
1 TATTATTATTATTATTATTAT-T
*
276381 GATTATTATTATTATTATTATT
1 TATTATTATTATTATTATTATT
*
276403 TATTATTATTATTATTAATATT
1 TATTATTATTATTATTATTATT
276425 TATTA
1 TATTA
276430 CAACTATTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
20 9 0.15
21 7 0.11
22 40 0.65
23 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (22 bp):
TATTATTATTATTATTATTATT
Found at i:283968 original size:15 final size:16
Alignment explanation
Indices: 283948--283977 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
283938 TTTAGTATTG
283948 AAGAAGAAGA-AGAAA
1 AAGAAGAAGATAGAAA
283963 AAGAAGAAGATAGAA
1 AAGAAGAAGATAGAA
283978 GGCCTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (16 bp):
AAGAAGAAGATAGAAA
Found at i:285122 original size:8 final size:8
Alignment explanation
Indices: 285103--285180 Score: 58
Period size: 9 Copynumber: 9.8 Consensus size: 8
285093 TTAAAGATAA
285103 AAAAAATG
1 AAAAAATG
285111 -AAAAATG
1 AAAAAATG
*
285118 AAAAAAATAAA
1 -AAAAAAT--G
285129 AAAAAATG
1 AAAAAATG
285137 AAAAAATG
1 AAAAAATG
*
285145 -AAATA-G
1 AAAAAATG
285151 -AAAAATAG
1 AAAAAAT-G
285159 AAAAAATGG
1 AAAAAAT-G
285168 AAAAAAT-
1 AAAAAATG
285175 AAAAAA
1 AAAAAA
285181 GAAGAAGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
6 5 0.09
7 17 0.29
8 9 0.16
9 20 0.34
10 7 0.12
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:285194 original size:31 final size:30
Alignment explanation
Indices: 285149--285207 Score: 59
Period size: 31 Copynumber: 2.0 Consensus size: 30
285139 AAAATGAAAT
* *
285149 AGAAAAATAGAAAAAATGGAAAAAATAAAAA
1 AGAAAAAGAAAAAAAAT-GAAAAAATAAAAA
*
285180 AGAAGAAGAAAAAAACA--AAAAAATAAAA
1 AGAAAAAGAAAAAAA-ATGAAAAAATAAAA
285208 GGGGGGTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
29 11 0.46
31 12 0.50
32 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.07
Consensus pattern (30 bp):
AGAAAAAGAAAAAAAATGAAAAAATAAAAA
Found at i:286571 original size:55 final size:55
Alignment explanation
Indices: 286487--286766 Score: 474
Period size: 55 Copynumber: 5.1 Consensus size: 55
286477 TGAAACAAAA
286487 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
286542 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
286597 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
286650 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCAATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
286705 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
286760 GGAGATT
1 GAAGATT
286767 ATTGTTCGAG
Statistics
Matches: 208, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
53 47 0.23
54 6 0.03
55 155 0.75
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:286690 original size:108 final size:110
Alignment explanation
Indices: 286487--286769 Score: 498
Period size: 108 Copynumber: 2.6 Consensus size: 110
286477 TGAAACAAAA
286487 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
*
286552 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGAT
* *
286597 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
286660 CGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCAATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGAT
*
286705 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
286770 GTTCGAGTTC
Statistics
Matches: 163, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
108 100 0.61
109 6 0.04
110 57 0.35
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGAT
Found at i:286822 original size:52 final size:52
Alignment explanation
Indices: 286762--287210 Score: 763
Period size: 52 Copynumber: 8.6 Consensus size: 52
286752 CGATCGTTGG
*
286762 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAAGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
286814 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
286866 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
286918 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * *
286970 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
287022 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
287074 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
287126 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
287178 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
287211 TAGAGAGCGA
Statistics
Matches: 376, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 376 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Done.