Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003856.1 Hibiscus syriacus cultivar Beakdansim tig00008289_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: 822684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:4277 original size:20 final size:19
Alignment explanation
Indices: 4239--4286 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
4229 CAAGAAGTAC
* *
4239 CGATATTGCTTAGGTAGTG
1 CGATACTGCTTAGGCAGTG
*
4258 TCGATACTGCTTATGCAGTG
1 -CGATACTGCTTAGGCAGTG
4278 CTGATACTG
1 C-GATACTG
4287 TCGAGGCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (19 bp):
CGATACTGCTTAGGCAGTG
Found at i:4398 original size:21 final size:24
Alignment explanation
Indices: 4345--4404 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
4335 TACCATATAC
4345 GGTATCGATACTACTTAGTGTAGT
1 GGTATCGATACTACTTAGTGTAGT
*
4369 AGTATCGATACT-CTTAGT-TA-T
1 GGTATCGATACTACTTAGTGTAGT
* *
4390 GGTACCGATAATACT
1 GGTATCGATACTACT
4405 CCTTTTGGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.32
22 4 0.13
23 6 0.19
24 11 0.35
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (24 bp):
GGTATCGATACTACTTAGTGTAGT
Found at i:4852 original size:65 final size:65
Alignment explanation
Indices: 4696--4852 Score: 169
Period size: 65 Copynumber: 2.4 Consensus size: 65
4686 AAATAGCCAG
* * * *
4696 AGTGCATCAATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTATTATAAAATCATC
* * * *
4761 AGTGCATCGATGCATTGTAT-GAGCATCGATGCATGAAATGCATTCGATGTTCAATT-T-AATTC
1 AGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGTT--ATTATAAAATC
4823 AT-
63 ATC
*
4825 GGTGCATCGATGCATGGATTGGTGCATC
1 AGTGCATCGATGCATGG-TTGGTGCATC
4853 AGTCACTACA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
64 16 0.21
65 56 0.74
66 2 0.03
67 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (65 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTATTATAAAATCATC
Found at i:5056 original size:41 final size:41
Alignment explanation
Indices: 4934--5326 Score: 395
Period size: 41 Copynumber: 9.5 Consensus size: 41
4924 TACATATAGC
* * *
4934 GGCGTTTTTGA-ACAAACGCCGCAAAATACTA-TACTTTAGT
1 GGCGTTTTT-ATACAAACGCCGCTATAGACTAGTACTTTAGT
* * * * * * * * *
4974 GACGTTTGTATAAAAATGCCGCTAAAGAATCGTAATGTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGT
* *
5015 GGCGTTTTTATACAAACGCCGCTATAAACTAGTATTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGT
* * *
5056 GGCGTTTTTATTCAAACGCCGCTATAGAC-ACATACTTTTGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTA-GTACTTTAGT
* * *
5097 GGCATTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATA-CAAACGCCGCTATAGACTAGTACTTTAGT
*
5139 GGCATTTTTATACAAACGCCGCTATAGAC-ACGTACATTT-GT
1 GGCGTTTTTATACAAACGCCGCTATAGACTA-GTAC-TTTAGT
* * *
5180 GGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGT
1 GGCGTTTTTATA-CAAACGCCGCTATAGACTAGTACTTTAGT
* *
5222 GGCGTTTTTACACAAACGCCGCTATAGAC-ACGTACTTTTGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTA-GTACTTTAGT
* *
5263 GGCG-TTTTAAACCAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATA-CAAACGCCGCTATAGACTAGTACTTTAGT
*
5304 GGCGTTTTAATACCAAACGCCGC
1 GGCGTTTTTATA-CAAACGCCGC
5327 AATTGTCATA
Statistics
Matches: 292, Mismatches: 47, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.00
40 28 0.10
41 176 0.60
42 87 0.30
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGT
Found at i:5138 original size:83 final size:83
Alignment explanation
Indices: 4965--5326 Score: 505
Period size: 83 Copynumber: 4.4 Consensus size: 83
4955 CAAAATACTA
* * * * * * * * *
4965 TACTTTAGTGACGTTTGTATAAAAATGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-C
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATACC
* *
5028 AAACGCCGCTATAAACTAG
65 AAACGCCGCTATAGACTCG
* * * *
5047 TATTTTAGTGGCGTTTTTATTCAAACGCCGCTATAGACACATACTTTTGTGGCATTTTAATACCA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
5112 AACGCCGCTATAGACTCG
66 AACGCCGCTATAGACTCG
* *
5130 TACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACACGTACATTTGTGGCGTTTTAATACCA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
*
5195 AACGCCGCTATAGATTCG
66 AACGCCGCTATAGACTCG
*
5213 TACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAA-ACCA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
5277 AACGCCGCTATAGACTCG
66 AACGCCGCTATAGACTCG
*
5295 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCGC
5327 AATTGTCATA
Statistics
Matches: 249, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
82 87 0.35
83 162 0.65
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (83 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
AACGCCGCTATAGACTCG
Found at i:5147 original size:124 final size:123
Alignment explanation
Indices: 4964--5326 Score: 410
Period size: 124 Copynumber: 2.9 Consensus size: 123
4954 GCAAAATACT
* * * * * * * * * *
4964 ATACTTTAGTGACGTTTGTATAAAAATGCCGCTAAAGAATCGTAATGTAGTGGCGTTTTTATACA
1 ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACTCGTACTTTAGTGGC-TTTTTATACA
* * * *
5029 AACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTTAT-TCAAACGCCGCTATAGACAC
65 AACGCCGCTATAGACTAGTAATTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACAC
*
5087 ATACTTTTGTGGCATTTTAATAC-CAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATA
1 ATACTTTAGTGGCATTTT--TACACAAACGCCGCTATAGACTCGTACTTTAGTGGC-TTTTTATA
**
5151 CAAACGCCGCTATAGAC-ACGTACATTT-GTGGCGTTTTAATACCAAACGCCGCTATAGATTC
63 CAAACGCCGCTATAGACTA-GTA-ATTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACAC
* * * * * *
5212 GTACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAAACCA
1 ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACTCGTACTTTAGTGGCTTTTTATA-CA
* *
5277 AACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATACCAAACGCCGC
65 AACGCCGCTATAGACTAGTAATTTAGTGGCGTTTTAATACCAAACGCCGC
5327 AATTGTCATA
Statistics
Matches: 204, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
123 27 0.13
124 140 0.69
125 37 0.18
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (123 bp):
ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACTCGTACTTTAGTGGCTTTTTATACAA
ACGCCGCTATAGACTAGTAATTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACAC
Found at i:8796 original size:43 final size:42
Alignment explanation
Indices: 8730--9053 Score: 337
Period size: 43 Copynumber: 7.6 Consensus size: 42
8720 AAGGTAATTA
* *
8730 GCGGTGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
* ** *
8773 GTGGCGTTTGTGTTTAAAAACGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
* *
8816 GCAGCGTTCGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
* *
8859 GCGGCGTTTGTTCTAAAAATGCCAG-TATAGGTCTG-CTCTTTT
1 GCGGCGTTTGTTCCAAAAACGCC-GCTATAGGTCTGAC-CTTTT
*
8901 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
* ** * * ** * *
8944 GCGGCGTTTTTTTTAAAAATGCCACTATATATCATAACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTC-TGACCTTTT
* *
8987 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTCT-GACCTTTT
** *
9030 GCGATGTTTGTTCAAAAAACGCCG
1 GCGGCGTTTGTTCCAAAAACGCCG
9054 TAATATATAT
Statistics
Matches: 234, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.00
42 55 0.24
43 177 0.76
44 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTCTGACCTTTT
Found at i:8924 original size:85 final size:85
Alignment explanation
Indices: 8730--9048 Score: 376
Period size: 85 Copynumber: 3.7 Consensus size: 85
8720 AAGGTAATTA
* * * * * *
8730 GCGGTGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGTGGCGTTTGTGTTTAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCTAAAAATG
8795 CC-GTTATAGGTCTGAC-CTTTT
65 CCAG-TATAGGTCTG-CTCTTTT
* * * *
8816 GCAGCGTTCGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAATGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAATGC
8881 CAGTATAGGTCTGCTCTTTT
66 CAGTATAGGTCTGCTCTTTT
* *
8901 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTTTTTAAAAATGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAATGC
* ** *
8966 CACTATATATCATAACT-TTTT
66 CAGTATAGGTC-T-GCTCTTTT
* ** *
8987 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGATGTTTGTTCAAAAAA
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAAAAA
9049 CGCCGTAATA
Statistics
Matches: 204, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.00
85 114 0.56
86 87 0.43
87 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (85 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAATGC
CAGTATAGGTCTGCTCTTTT
Found at i:9865 original size:2 final size:2
Alignment explanation
Indices: 9858--9885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9848 ACCAAACCAA
9858 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
9886 TAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9950 original size:14 final size:15
Alignment explanation
Indices: 9931--9960 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
9921 TTCAAACATT
9931 AAACAATCCA-AAAC
1 AAACAATCCAGAAAC
9945 AAACAATCCAGAAAC
1 AAACAATCCAGAAAC
9960 A
1 A
9961 TCAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.27, G:0.03, T:0.07
Consensus pattern (15 bp):
AAACAATCCAGAAAC
Found at i:11808 original size:11 final size:11
Alignment explanation
Indices: 11792--11816 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11782 GGCGGCCAAG
11792 AGAGAGTTTTA
1 AGAGAGTTTTA
11803 AGAGAGTTTTA
1 AGAGAGTTTTA
11814 AGA
1 AGA
11817 AAATGAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (11 bp):
AGAGAGTTTTA
Found at i:11906 original size:23 final size:22
Alignment explanation
Indices: 11878--11957 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
11868 GCACGGCCTT
11878 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
11900 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
11922 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
11944 ATGCATCGGTGCAC
1 GTGCATCGATGCAC
11958 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 16 0.35
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:15516 original size:18 final size:18
Alignment explanation
Indices: 15473--15510 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15463 GTGAAGTATG
*
15473 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
15491 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
15509 AA
1 AA
15511 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:21666 original size:21 final size:21
Alignment explanation
Indices: 21642--21683 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21632 AAATATAAAC
21642 ATAAGAA-GGAAATGATATGAA
1 ATAAGAATGGAAATGAT-TGAA
* *
21663 ATAATAATTGAAATGATTGAA
1 ATAAGAATGGAAATGATTGAA
21684 TGAAAAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (21 bp):
ATAAGAATGGAAATGATTGAA
Found at i:21814 original size:18 final size:18
Alignment explanation
Indices: 21771--21808 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21761 GTGAAGTATG
*
21771 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
21789 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
21807 AA
1 AA
21809 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:25731 original size:46 final size:44
Alignment explanation
Indices: 25633--25735 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
25623 GTGCACTAAG
* * *
25633 AGTGCACCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCA
1 AGTGCATCGATGAATCAAATGCATTCGATGTTTCAAAATAGCCA
25677 GAGTGCATCGATGAATCAAATGCATTCGATGTTTTCATAAAATA-CTC-
1 -AGTGCATCGATGAATCAAATGCATTCGATG-TTTC--AAAATAGC-CA
25724 AGTGCATCGATG
1 AGTGCATCGATG
25736 CATGGTATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 27 0.53
46 16 0.31
47 1 0.02
48 7 0.14
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AGTGCATCGATGAATCAAATGCATTCGATGTTTCAAAATAGCCA
Found at i:29167 original size:45 final size:45
Alignment explanation
Indices: 29105--29201 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
29095 TTTGGAAACA
*
29105 AAAATAAT-TAAATAA-T-TATTTATATATATTTATAAAATATATATT
1 AAAATATTCTAAATAATTATATTTATA-ATA-TTATAAAAT-TATATT
* **
29150 AAATTATTCTAAA-AATTATATTTATAATATTATGGAATTATATT
1 AAAATATTCTAAATAATTATATTTATAATATTATAAAATTATATT
29194 AAAATATT
1 AAAATATT
29202 TATTTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
44 13 0.30
45 15 0.34
46 8 0.18
47 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (45 bp):
AAAATATTCTAAATAATTATATTTATAATATTATAAAATTATATT
Found at i:29169 original size:22 final size:22
Alignment explanation
Indices: 29112--29171 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
29102 ACAAAAATAA
*
29112 TTAAATAATTAT-TTATATATAT
1 TTAAA-AATTATATTAAATATAT
29134 TTATAAAATATATATTAAAT-TAT
1 TTA-AAAAT-TATATTAAATATAT
29157 TCTAAAAATTATATT
1 T-TAAAAATTATATT
29172 TATAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 12 0.36
23 14 0.42
24 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAAATTATATTAAATATAT
Found at i:29180 original size:23 final size:22
Alignment explanation
Indices: 29121--29180 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
29111 ATTAAATAAT
29121 TATTTATATATATTTATAAAATA
1 TATTTATA-ATATTTATAAAATA
29144 TATATTA-AATTATTCTA-AAAATTA
1 TAT-TTATAA-TATT-TATAAAA-TA
29168 TATTTATAATATT
1 TATTTATAATATT
29181 ATGGAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 1 0.03
23 19 0.59
24 12 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTATAATATTTATAAAATA
Found at i:29210 original size:22 final size:21
Alignment explanation
Indices: 29168--29256 Score: 69
Period size: 22 Copynumber: 4.3 Consensus size: 21
29158 CTAAAAATTA
* **
29168 TATTTATAATA-TTATGGAAT
1 TATTTAAAATATTTATTTAAT
29188 TATATTAAAATATTTATTTAAT
1 TAT-TTAAAATATTTATTTAAT
*
29210 T-TTTAAAATCATATTATTTATT
1 TATTTAAAAT-AT-TTATTTAAT
* *
29232 TATTTGAAATA-ATA-TTAAT
1 TATTTAAAATATTTATTTAAT
29251 TATTTA
1 TATTTA
29257 TTTGAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.16
20 12 0.21
21 10 0.18
22 18 0.32
23 7 0.12
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTAAAATATTTATTTAAT
Found at i:29241 original size:23 final size:23
Alignment explanation
Indices: 29196--29272 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
29186 ATTATATTAA
* *
29196 AATATTTATTTAATT-TTTAAAAT
1 AATA-TTATTTATTTATTTGAAAT
*
29219 CATATTATTTATTTATTTGAAAT
1 AATATTATTTATTTATTTGAAAT
*
29242 AATATTAATTATTTATTTGAAAT
1 AATATTATTTATTTATTTGAAAT
29265 AATATTAT
1 AATATTAT
29273 ACAGAACCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.19
23 38 0.81
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
AATATTATTTATTTATTTGAAAT
Found at i:29342 original size:16 final size:16
Alignment explanation
Indices: 29323--29368 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
29313 ATCTTAAATT
29323 TAAAATTATTTAAAAA
1 TAAAATTATTTAAAAA
29339 TAAATATATAATTTAAAAA
1 TAAA-AT-T-ATTTAAAAA
*
29358 TAATATTATTT
1 TAAAATTATTT
29369 CAAATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 8 0.31
17 3 0.12
18 3 0.12
19 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTATTTAAAAA
Found at i:29377 original size:19 final size:18
Alignment explanation
Indices: 29336--29386 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
29326 AATTATTTAA
29336 AAATAAAT-ATATAATTT
1 AAATAAATAATATAATTT
*
29353 -AA-AAATAATATTATTT
1 AAATAAATAATATAATTT
29369 CAAATAAATAAT-TAATTT
1 -AAATAAATAATATAATTT
29387 GATTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
18 7 0.25
19 7 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAAATAATATAATTT
Found at i:33447 original size:22 final size:22
Alignment explanation
Indices: 33416--33457 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33406 TTTATACTTG
*
33416 AAATTTAAATAAAAGAAATATT
1 AAATTAAAATAAAAGAAATATT
* *
33438 AAATTAAAATATAATAAATA
1 AAATTAAAATAAAAGAAATA
33458 ATTTAAGAAA
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:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATTAAAATAAAAGAAATATT
Found at i:36100 original size:43 final size:43
Alignment explanation
Indices: 36052--36141 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
36042 ACATAAAAAA
*
36052 TTATATTTATTGATAAAAGTTATAGTTTTGTAAGTTTTTATTT
1 TTATATTTATTGATAAAAGATATAGTTTTGTAAGTTTTTATTT
36095 TTATATTTATTGATAAAAGATATAGTTTTGTAAGTTTTTATTT
1 TTATATTTATTGATAAAAGATATAGTTTTGTAAGTTTTTATTT
36138 TTAT
1 TTAT
36142 TAACATAGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (43 bp):
TTATATTTATTGATAAAAGATATAGTTTTGTAAGTTTTTATTT
Found at i:48041 original size:25 final size:25
Alignment explanation
Indices: 48007--48065 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
47997 CGTCATAACA
48007 AACTAACTAAAGTTGTTAGTCTACT
1 AACTAACTAAAGTTGTTAGTCTACT
48032 AACTAACTAAAGTTGTTAGTCTACT
1 AACTAACTAAAGTTGTTAGTCTACT
48057 AACTAACTA
1 AACTAACTA
48066 TGCTGAGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (25 bp):
AACTAACTAAAGTTGTTAGTCTACT
Found at i:53533 original size:40 final size:35
Alignment explanation
Indices: 53453--53528 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
53443 AAAACAGTCC
*
53453 TCAATTTCATTCTAAACCCCAATTTCCAATGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAATGTAAT
* **
53488 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAATGTAAT
53523 TCAATT
1 TCAATT
53529 CAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAATGTAAT
Found at i:54066 original size:130 final size:130
Alignment explanation
Indices: 53917--54164 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
53907 TCTTTATATA
* **
53917 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
53982 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
54047 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
54112 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
54165 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:54195 original size:130 final size:129
Alignment explanation
Indices: 53931--54195 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
53921 ATTTGGTCCT
* ** *
53931 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
53996 TGACACGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
54061 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
54126 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
54190 -A
128 CA
54191 AAATT
1 AAATT
54196 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:54656 original size:16 final size:18
Alignment explanation
Indices: 54635--54667 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54625 ATTTCTTATT
54635 AAAATA-AAAT-ATTCAA
1 AAAATATAAATGATTCAA
54651 AAAATATAAATGATTCA
1 AAAATATAAATGATTCA
54668 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAATATAAATGATTCAA
Found at i:61485 original size:31 final size:31
Alignment explanation
Indices: 61450--61511 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
61440 CCTTGTATTT
61450 TGATCTGTGCTCCTCAAATGTATATTCATTC
1 TGATCTGTGCTCCTCAAATGTATATTCATTC
61481 TGATCTGTGCTCCTCAAATGTATATTCATTC
1 TGATCTGTGCTCCTCAAATGTATATTCATTC
61512 CTTTTCTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (31 bp):
TGATCTGTGCTCCTCAAATGTATATTCATTC
Found at i:71989 original size:2 final size:2
Alignment explanation
Indices: 71982--72006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71972 TTTTGTAAAA
71982 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
72007 ATTTTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72545 original size:27 final size:27
Alignment explanation
Indices: 72485--72558 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
72475 CTGAATTGAC
* *
72485 TAAAATAACCAAAATACCTTCGAGCTT
1 TAAAATGACCAAAATACCCTCGAGCTT
*
72512 TAAAATGACCAAAATACCCTCGAGTTT
1 TAAAATGACCAAAATACCCTCGAGCTT
** *
72539 TGGAATGACCTAAATACCCT
1 TAAAATGACCAAAATACCCT
72559 TATGTATTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.26
Consensus pattern (27 bp):
TAAAATGACCAAAATACCCTCGAGCTT
Found at i:75910 original size:24 final size:24
Alignment explanation
Indices: 75883--75937 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
75873 CAATCTCCGA
75883 GATCTATCTTTATACGACTCTTTC
1 GATCTATCTTTATACGACTCTTTC
75907 GATCTATCTTTATACGACTCTTTC
1 GATCTATCTTTATACGACTCTTTC
75931 GATCTAT
1 GATCTAT
75938 ATACTTCCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (24 bp):
GATCTATCTTTATACGACTCTTTC
Found at i:77674 original size:34 final size:32
Alignment explanation
Indices: 77594--77675 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
77584 TTATTATTTT
* *
77594 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTATATTTTATATTAATATA
* *
77626 ATTATATAAATATTATATTTT-TATTAAAATAATA
1 TTTATATAATTATTATATTTTATATT--AAT-ATA
77660 TTTATATAATTATTAT
1 TTTATATAATTATTAT
77676 TTATTTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 4 0.10
32 17 0.41
33 3 0.07
34 17 0.41
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTATATAATTATTATATTTTATATTAATATA
Found at i:82117 original size:11 final size:11
Alignment explanation
Indices: 82103--82130 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
82093 TTTCAAATTC
82103 ATTTTTCTTTT
1 ATTTTTCTTTT
82114 ATTTTTCTTTT
1 ATTTTTCTTTT
82125 ATTTTT
1 ATTTTT
82131 TCATTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:84792 original size:20 final size:20
Alignment explanation
Indices: 84735--84797 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
84725 ATTAAGAGTG
*
84735 GTAAATGAATGCAAATTAGT
1 GTAAATGAATGCAAATTGGT
**
84755 GCGAATGAATGCAAATTGGT
1 GTAAATGAATGCAAATTGGT
84775 GTAAATGAATGCAAATTGGT
1 GTAAATGAATGCAAATTGGT
84795 GTA
1 GTA
84798 GAAGTGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (20 bp):
GTAAATGAATGCAAATTGGT
Found at i:85709 original size:21 final size:21
Alignment explanation
Indices: 85646--85702 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
85636 TCGAGGGTCT
* *
85646 TATGTGGTCCTTCGGGATAAA
1 TATGTGGTCATTCGGGACAAA
85667 TATGTGGTCATTCGGGACAAA
1 TATGTGGTCATTCGGGACAAA
85688 TATGTGG-CACTTCGG
1 TATGTGGTCA-TTCGG
85703 TGCAAATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACAAA
Found at i:91049 original size:20 final size:20
Alignment explanation
Indices: 91013--91063 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
91003 GTTGATAGTG
*
91013 GTATCGATA-CTGTAAGGGT
1 GTATCGATACCTGTAAGGAT
91032 AGTATCGATACCTG-AAGGAT
1 -GTATCGATACCTGTAAGGAT
91052 GATATCGATACC
1 G-TATCGATACC
91064 CTTAAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.86
21 3 0.11
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (20 bp):
GTATCGATACCTGTAAGGAT
Found at i:91175 original size:54 final size:54
Alignment explanation
Indices: 91054--91177 Score: 169
Period size: 54 Copynumber: 2.3 Consensus size: 54
91044 TGAAGGATGA
* *
91054 TATCGATACCCTTAAAACATCGAATGCCAGATTGGTATCAGTACCTTGAGGAGG
1 TATCGATACCCTTGAAACATCGAATGCCAGATTGGTATCAGTACCATGAGGAGG
** * *
91108 TATCGATACCCTTGAAACATCGAATGTTA-TTTCGGTATCGGTACCATGAGGAGG
1 TATCGATACCCTTGAAACATCGAATGCCAGATT-GGTATCAGTACCATGAGGAGG
*
91162 TATCAATACCCTTGAA
1 TATCGATACCCTTGAA
91178 GGGTAGTATC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 2 0.03
54 60 0.97
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (54 bp):
TATCGATACCCTTGAAACATCGAATGCCAGATTGGTATCAGTACCATGAGGAGG
Found at i:91719 original size:21 final size:21
Alignment explanation
Indices: 91693--91764 Score: 85
Period size: 21 Copynumber: 3.3 Consensus size: 21
91683 TCGAGGGTCT
91693 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
91714 TATGTGG-CACTTCGGTGA-AAA
1 TATGTGGTC-CTTCGG-GACAAA
*
91735 CCTATGTGGTCATTCGGGACAAA
1 --TATGTGGTCCTTCGGGACAAA
91758 TATGTGG
1 TATGTGG
91765 CACTTTGGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
20 1 0.02
21 23 0.52
22 4 0.09
23 15 0.34
24 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:91742 original size:23 final size:22
Alignment explanation
Indices: 91693--91774 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 22
91683 TCGAGGGTCT
91693 TATGTGGTC-CTTCGG-GACAAA
1 TATGTGG-CACTTCGGTGACAAA
91714 TATGTGGCACTTCGGTGA-AAA
1 TATGTGGCACTTCGGTGACAAA
91735 CCTATGTGGTCA-TTCGG-GACAAA
1 --TATGTGG-CACTTCGGTGACAAA
*
91758 TATGTGGCACTTTGGTG
1 TATGTGGCACTTCGGTG
91775 TAAATTACGA
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
20 3 0.06
21 27 0.52
22 5 0.10
23 15 0.29
24 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGACAAA
Found at i:104721 original size:22 final size:20
Alignment explanation
Indices: 104688--104740 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
104678 TCCCTGATAT
*
104688 TTGTTTACTGATTTTATATTC
1 TTGTTTACTGA-TATATATTC
104709 TTGTTTGACTGATATATATTC
1 TTGTTT-ACTGATATATATTC
*
104730 TCTGGTTACTG
1 T-TGTTTACTG
104741 TTTACTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.55
Consensus pattern (20 bp):
TTGTTTACTGATATATATTC
Found at i:113268 original size:32 final size:33
Alignment explanation
Indices: 113232--113393 Score: 172
Period size: 32 Copynumber: 5.1 Consensus size: 33
113222 CACTCTTGCT
* *
113232 CATTATCTGAATGCAACACTGACCT-TACTGTG
1 CATTATCTGAATGTAACACTGACCTCTACTATG
* * *
113264 CATTATCTGAATGCAACACTGACCT-TATTGTG
1 CATTATCTGAATGTAACACTGACCTCTACTATG
* *
113296 CATTATCTGAATGTTACACTGA-CTCTATTATG
1 CATTATCTGAATGTAACACTGACCTCTACTATG
* * *
113328 CATTATATGAATGTAACACT-AACTCTGCTATG
1 CATTATCTGAATGTAACACTGACCTCTACTATG
* * *
113360 CTTTATATGAATGTAACACTGA-CACTACTATG
1 CATTATCTGAATGTAACACTGACCTCTACTATG
113392 CA
1 CA
113394 ACACACAATC
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
31 3 0.03
32 111 0.97
33 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (33 bp):
CATTATCTGAATGTAACACTGACCTCTACTATG
Found at i:114632 original size:45 final size:45
Alignment explanation
Indices: 114598--114793 Score: 227
Period size: 45 Copynumber: 4.4 Consensus size: 45
114588 AATACAGGTG
* *
114598 CATTATCAGCATGAAATG-ATGCTATAGTTGAAATGTATATGGGTA
1 CATTATCAACA-GAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* * * **
114643 CATTCTCAACAGAAAAGTAAGC-ACTGGTTGAAATGTATAAAGGTA
1 CATTATCAACAGAAAAGTATGCTA-TAGTTGAAATGTATATGGGTA
*
114688 CATTATCAACA-ATAAAGTATACTATAGTTGAAATGTATATGGGTA
1 CATTATCAACAGA-AAAGTATGCTATAGTTGAAATGTATATGGGTA
* * * *
114733 CATTATCAACAGAAAAGTATGTTATTGTTGAAATGCATATGGGTG
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
*
114778 CATTATCAACATAAAA
1 CATTATCAACAGAAAA
114794 ATATATTATG
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
44 7 0.06
45 118 0.93
46 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (45 bp):
CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
Found at i:114763 original size:90 final size:89
Alignment explanation
Indices: 114583--114792 Score: 253
Period size: 90 Copynumber: 2.3 Consensus size: 89
114573 TGAAAAATTA
* * * * *
114583 AAATGAATACAGGTGCATTATCAGCATGAAA-TGATGCTATAGTTGAAATGTATATGGGTACATT
1 AAATGCATAAAGGTACATTATCAACAT-AAAGT-ATACTATAGTTGAAATGTATATGGGTACATT
*
114647 CTCAACAGAAAAGTAAGCACTGGTTG
64 ATCAACAGAAAAGTAAGCACTGGTTG
*
114673 AAATGTATAAAGGTACATTATCAACAATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
1 AAATGCATAAAGGTACATTATCAAC-ATAAAGTATACTATAGTTGAAATGTATATGGGTACATTA
* * *
114738 TCAACAGAAAAGTATGTTA-TTGTTG
65 TCAACAGAAAAGTAAG-CACTGGTTG
** *
114763 AAATGCATATGGGTGCATTATCAACATAAA
1 AAATGCATAAAGGTACATTATCAACATAAA
114793 AATATATTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
89 5 0.05
90 95 0.91
91 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.30
Consensus pattern (89 bp):
AAATGCATAAAGGTACATTATCAACATAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
CAACAGAAAAGTAAGCACTGGTTG
Found at i:114819 original size:45 final size:45
Alignment explanation
Indices: 114688--114837 Score: 144
Period size: 45 Copynumber: 3.3 Consensus size: 45
114678 TATAAAGGTA
* * * * * *
114688 CATTATCAACA-ATAAAGTATACTATAGTTGAAATGTATATGGGTA
1 CATTATCAACATA-AAAATATATTATTGCTGAAATGCATATGGGTG
* * * *
114733 CATTATCAACAGAAAAGTATGTTATTGTTGAAATGCATATGGGTG
1 CATTATCAACATAAAAATATATTATTGCTGAAATGCATATGGGTG
*
114778 CATTATCAACATAAAAATATATTA-TGACT-AAATTGCTTATGGGTG
1 CATTATCAACATAAAAATATATTATTG-CTGAAA-TGCATATGGGTG
*
114823 CATTATTAACATAAA
1 CATTATCAACATAAA
114838 GGCATGATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
44 5 0.05
45 85 0.93
46 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (45 bp):
CATTATCAACATAAAAATATATTATTGCTGAAATGCATATGGGTG
Found at i:121491 original size:45 final size:45
Alignment explanation
Indices: 121454--121682 Score: 291
Period size: 45 Copynumber: 5.1 Consensus size: 45
121444 TTATCAGTAT
* * * * *
121454 GAAAAG-ATGTTATAGTTGAAATGCATATGGGCACATTATTAAAA
1 GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACA
*
121498 GAAAAGTAAGC-ACTAGTTGAAATGTATATGGGTACATTATCAACA
1 GAAAAGTATGCTA-TAGTTGAAATGTATATGGGTACATTATCAACA
* * *
121543 GTAAAGTATTCTATAGTTGAAATGTATATGGGTACATTATCAATA
1 GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACA
*
121588 GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATAATCAACA
1 GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACA
* * * * *
121633 AAAAAGTATGCTATTGTAGAAATGCATATGGGTGCATTATCAACA
1 GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACA
*
121678 TAAAA
1 GAAAA
121683 ATATATTATG
Statistics
Matches: 161, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
44 7 0.04
45 153 0.95
46 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (45 bp):
GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATTATCAACA
Found at i:121716 original size:135 final size:135
Alignment explanation
Indices: 121438--121717 Score: 313
Period size: 135 Copynumber: 2.1 Consensus size: 135
121428 AATGCATACA
* * * *
121438 GGTGCATTATCAGTATGAAAAGATGTTATAGTTGAAATGCATATGGGCACATTATTAAAAGAAAA
1 GGTGCATTATCAATATGAAAAGATGCTATAGTTGAAATGCATATGGGCACATAATCAAAAGAAAA
* * * *
121503 GTAAGCACTAGTTGAAATGTATATGGGTACATTATCAACAGTAAAGTATTCTATAGTTGAAATGT
66 GTAAGCACTAGTAGAAATGCATATGGGTACATTATCAACAGTAAAATATTCTATAGCTGAAATGT
121568 ATATG
131 ATATG
* * *
121573 GGTACATTATCAATA-GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATAATCAACAA-AA
1 GGTGCATTATCAATATGAAAAG-ATGCTATAGTTGAAATGCATATGGGCACATAATCAA-AAGAA
* * *
121636 AAGTATGCTA-TTGTAGAAATGCATATGGGTGCATTATCAACA-TAAAAATATAT-TAT-GACTG
64 AAGTAAGC-ACTAGTAGAAATGCATATGGGTACATTATCAACAGT-AAAATAT-TCTATAG-CTG
*
121697 AATTGCT-TATG
125 AAATG-TATATG
121708 GGTGCATTAT
1 GGTGCATTAT
121718 TAACATAAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
134 8 0.07
135 109 0.89
136 5 0.04
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (135 bp):
GGTGCATTATCAATATGAAAAGATGCTATAGTTGAAATGCATATGGGCACATAATCAAAAGAAAA
GTAAGCACTAGTAGAAATGCATATGGGTACATTATCAACAGTAAAATATTCTATAGCTGAAATGT
ATATG
Found at i:124536 original size:17 final size:16
Alignment explanation
Indices: 124514--124548 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
124504 TATTAAAAAA
124514 AATAAAAAAAATAATAT
1 AATAAAAAAAAT-ATAT
*
124531 AATAAAAAATATATAT
1 AATAAAAAAAATATAT
124547 AA
1 AA
124549 AAGTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAAAAAATATAT
Found at i:124539 original size:16 final size:16
Alignment explanation
Indices: 124515--124548 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
124505 ATTAAAAAAA
124515 ATAA-AAAAAATA-AT
1 ATAATAAAAAATATAT
124529 ATAATAAAAAATATAT
1 ATAATAAAAAATATAT
124545 ATAA
1 ATAA
124549 AAGTATCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAATAAAAAATATAT
Found at i:126932 original size:25 final size:27
Alignment explanation
Indices: 126892--126941 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
126882 GAGAGTATTT
126892 TTAATTTAGATATTTAAATATTTTTTG
1 TTAATTTAGATATTTAAATATTTTTTG
*
126919 TTAA-TTAGAT-TTTAAATGTTTTT
1 TTAATTTAGATATTTAAATATTTTT
126942 AACATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 6 0.27
27 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (27 bp):
TTAATTTAGATATTTAAATATTTTTTG
Found at i:127709 original size:25 final size:24
Alignment explanation
Indices: 127678--127743 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
127668 TATAAAAAAA
127678 TTATAAAAGT-ATTATAAGAAT-ATAT
1 TTATAAAA-TAATT-TAA-AATAATAT
127703 TTATAAAATAATTTAAAATAATAT
1 TTATAAAATAATTTAAAATAATAT
127727 TTGAT-AAATAATATTAA
1 TT-ATAAAATAAT-TTAA
127744 TTATTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
23 3 0.08
24 17 0.46
25 17 0.46
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
TTATAAAATAATTTAAAATAATAT
Found at i:127815 original size:17 final size:17
Alignment explanation
Indices: 127785--127817 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
127775 TTAAAAAATT
127785 TTAAAATATATTTATTA
1 TTAAAATATATTTATTA
127802 TTAATAATAT-TTTATT
1 TTAA-AATATATTTATT
127818 TAGGTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAAATATATTTATTA
Found at i:128048 original size:2 final size:2
Alignment explanation
Indices: 128041--128078 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
128031 TCCTCTTGTA
128041 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
128079 TGAGGAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136803 original size:30 final size:29
Alignment explanation
Indices: 136769--136828 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
136759 AAATAGATTT
* *
136769 AGTTTAGTGACCAAATTATAAGATTTTGAA
1 AGTTTAGTGACCAAAGTATAA-ATCTTGAA
*
136799 AGTTTGGTGACCAAAGTATAAATCTTGAA
1 AGTTTAGTGACCAAAGTATAAATCTTGAA
136828 A
1 A
136829 AAGTTTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (29 bp):
AGTTTAGTGACCAAAGTATAAATCTTGAA
Found at i:139279 original size:23 final size:24
Alignment explanation
Indices: 139249--139294 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
139239 TTTTTTCTTT
*
139249 TACGTTTATTATTA-ATATTTTTA
1 TACGTTTATTACTATATATTTTTA
139272 TACGTTTATTACTATATATTTTT
1 TACGTTTATTACTATATATTTTT
139295 TAGTTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (24 bp):
TACGTTTATTACTATATATTTTTA
Found at i:139295 original size:26 final size:23
Alignment explanation
Indices: 139240--139296 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
139230 AATCTTTATT
*
139240 TTTTTCTTTTACGTTTATTATTAA
1 TTTTT-TTATACGTTTATTATTAA
* *
139264 TATTTTTATACGTTTATTACTATA
1 TTTTTTTATACGTTTATTATTA-A
139288 TATTTTTTA
1 T-TTTTTTA
139297 GTTATTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 15 0.56
24 6 0.22
25 6 0.22
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTTTTATACGTTTATTATTAA
Found at i:140517 original size:10 final size:10
Alignment explanation
Indices: 140481--140509 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
140471 TCCTTTACCA
140481 TTTATTTATT
1 TTTATTTATT
140491 TTTATTTATT
1 TTTATTTATT
140501 TTTATTTAT
1 TTTATTTAT
140510 CTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:150812 original size:105 final size:105
Alignment explanation
Indices: 150630--151505 Score: 1540
Period size: 105 Copynumber: 8.3 Consensus size: 105
150620 AGGTTTTACC
150630 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
150695 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
150735 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
150800 ACGAAGGGACCGCTGGTTATCAACAAACATTTCTCA-ATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
* *
150839 CAGAGCCAATTTCAACTTCACAACGAAGGATATTTGACTCCAGACAACGCAAATTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
150904 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
* *
150944 CAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
151009 ACGAAGGGACTGTTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
151049 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
151114 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
151154 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
151219 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
151259 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
151324 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
151364 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
151429 ACGAAGGGACTGCTGGTTGTCAACAAACAATTTC-CCGATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAGA-TT
* * * *
151470 CGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
151506 CCTCGAAACA
Statistics
Matches: 742, Mismatches: 26, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
104 100 0.13
105 603 0.81
106 39 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
Found at i:154862 original size:33 final size:33
Alignment explanation
Indices: 154820--154956 Score: 229
Period size: 33 Copynumber: 4.2 Consensus size: 33
154810 GAGTTATATG
* *
154820 ACAAAGATCTATGAGATCATACAAGAATGGTAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
154853 ACAAGGATCTATGAGATCATACAAGAATGTTAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
*
154886 ACAATGATCTATGAGATCATACAAGAATGTTAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
* *
154919 ACAAGGATCTATGAGATCACACAAGAATGTTAT
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
154952 ACAAG
1 ACAAG
154957 CTACATGATA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 98 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (33 bp):
ACAAGGATCTATGAGATCATACAAGAATGTTAC
Found at i:155258 original size:21 final size:21
Alignment explanation
Indices: 155211--155261 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
155201 GATATATACA
155211 AGGTCCTTCAGGACATACATG
1 AGGTCCTTCAGGACATACATG
** ** *
155232 TCGTCCTTTGGGACATATATG
1 AGGTCCTTCAGGACATACATG
155253 AGGTCCTTC
1 AGGTCCTTC
155262 GAGATATACA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (21 bp):
AGGTCCTTCAGGACATACATG
Found at i:155574 original size:28 final size:28
Alignment explanation
Indices: 155487--155574 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
155477 ATGATTCTAT
*
155487 ATGTTACAAATGTTAATTACAAGATGAC
1 ATGTTACAAATGTTAAGTACAAGATGAC
* * *
155515 ATATTACAAATGTTAAGTGCTAGATGAC
1 ATGTTACAAATGTTAAGTACAAGATGAC
* *
155543 ATGTTACAAA-GATTAAGCACAAGATGAT
1 ATGTTACAAATG-TTAAGTACAAGATGAC
155571 ATGT
1 ATGT
155575 CTTTAATGGG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.02
28 49 0.98
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (28 bp):
ATGTTACAAATGTTAAGTACAAGATGAC
Found at i:161129 original size:30 final size:31
Alignment explanation
Indices: 161095--161155 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
161085 TAGCAAAATT
* *
161095 GGGGACCATTTTG-TAATTTTTGAAAAGTTA
1 GGGGACCAATTTGATAATTTTGGAAAAGTTA
161125 GGGGACCAATTTGATAATTTTGGAAAAGTTA
1 GGGGACCAATTTGATAATTTTGGAAAAGTTA
161156 TGAATGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (31 bp):
GGGGACCAATTTGATAATTTTGGAAAAGTTA
Found at i:162826 original size:33 final size:33
Alignment explanation
Indices: 162789--162924 Score: 245
Period size: 33 Copynumber: 4.1 Consensus size: 33
162779 GGGTTATATG
162789 ACAAAGATCTATGAGATCATACAAGAATGTTAC
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
162822 ACAAAGATCTATGAGATCATACAAGAATGTTAC
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
*
162855 ACAATGATCTATGAGATCATACAAGAATGTTAC
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
* *
162888 ACAATGATCTATGAGATCATACAAGAATGTTAT
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
162921 ACAA
1 ACAA
162925 GCTACATGAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 101 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (33 bp):
ACAAAGATCTATGAGATCATACAAGAATGTTAC
Found at i:163271 original size:42 final size:42
Alignment explanation
Indices: 163191--163286 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
163181 GGTTATCCGA
* * *
163191 GACATATACAAGGTCATTCGGAACATACATGTCATCCTTTGG
1 GACATATACGAGGTCATTCGGAACATACAAGTCATCCTTCGG
* * **
163233 GACATATACGAGGTCCTTCGGGACATACAAGTTGTCCTTCGG
1 GACATATACGAGGTCATTCGGAACATACAAGTCATCCTTCGG
**
163275 GTTATATACGAG
1 GACATATACGAG
163287 ATTCTCCAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (42 bp):
GACATATACGAGGTCATTCGGAACATACAAGTCATCCTTCGG
Found at i:163498 original size:13 final size:13
Alignment explanation
Indices: 163480--163521 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
163470 GATTCTATAT
163480 ATTACAAATGTTA
1 ATTACAAATGTTA
163493 ATTACAAGATGACTT-
1 ATTACAA-ATG--TTA
163508 ATTACAAATGTTA
1 ATTACAAATGTTA
163521 A
1 A
163522 GTGCAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.08
13 8 0.32
14 6 0.24
15 7 0.28
16 2 0.08
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (13 bp):
ATTACAAATGTTA
Found at i:163510 original size:28 final size:28
Alignment explanation
Indices: 163478--163560 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
163468 ATGATTCTAT
*
163478 ATATTACAAATGTTAATTACAAGATGAC
1 ATATTACAAATGTTAAGTACAAGATGAC
* *
163506 TTATTACAAATGTTAAGTGCAAGATGAC
1 ATATTACAAATGTTAAGTACAAGATGAC
* *
163534 ATGTTACAAA-GATGAAGTACAAGATGA
1 ATATTACAAATG-TTAAGTACAAGATGA
163561 TATGTCTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 46 0.98
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (28 bp):
ATATTACAAATGTTAAGTACAAGATGAC
Found at i:164458 original size:12 final size:12
Alignment explanation
Indices: 164438--164503 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
164428 ATATATCTTA
*
164438 ATCATCATCATC
1 ATCATCATCACC
*
164450 ATCACCATCACC
1 ATCATCATCACC
*
164462 ATCATCAAT-ATC
1 ATCATC-ATCACC
*
164474 ATCA-CTGTCACC
1 ATCATC-ATCACC
*
164486 ATCACCATCACC
1 ATCATCATCACC
164498 ATCATC
1 ATCATC
164504 GTCATCTCCA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
11 2 0.05
12 37 0.88
13 3 0.07
ACGTcount: A:0.33, C:0.39, G:0.02, T:0.26
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:164474 original size:24 final size:24
Alignment explanation
Indices: 164438--164501 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
164428 ATATATCTTA
164438 ATCATCATCATCATCACCATCACC
1 ATCATCATCATCATCACCATCACC
**
164462 ATCATCAAT-ATCATCACTGTCACC
1 ATCATC-ATCATCATCACCATCACC
* *
164486 ATCACCATCACCATCA
1 ATCATCATCATCATCA
164502 TCGTCATCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 30 0.88
25 2 0.06
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.25
Consensus pattern (24 bp):
ATCATCATCATCATCACCATCACC
Found at i:164507 original size:24 final size:24
Alignment explanation
Indices: 164438--164507 Score: 59
Period size: 30 Copynumber: 2.7 Consensus size: 24
164428 ATATATCTTA
* *
164438 ATCATCATCATCATCACCATCACC
1 ATCACCATCATCGTCACCATCACC
*
164462 ATCATCAATATCATCACTGTCACCATCACC
1 ATCA-C--CATCAT--C-GTCACCATCACC
164492 ATCACCATCATCGTCA
1 ATCACCATCATCGTCA
164508 TCTCCATCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
24 8 0.22
25 1 0.03
27 10 0.28
29 2 0.06
30 15 0.42
ACGTcount: A:0.33, C:0.39, G:0.03, T:0.26
Consensus pattern (24 bp):
ATCACCATCATCGTCACCATCACC
Found at i:168087 original size:32 final size:33
Alignment explanation
Indices: 168031--168093 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
168021 GGTCAATATC
*
168031 GGGTCGGGTCAATACCGGAGCAGTT-GATTTTT
1 GGGTCGGGTCAATACCAGAGCAGTTAGATTTTT
* * *
168063 GGGTCGGGTTAATATCAGATCAGTTAGATTT
1 GGGTCGGGTCAATACCAGAGCAGTTAGATTT
168094 CGGGTTGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (33 bp):
GGGTCGGGTCAATACCAGAGCAGTTAGATTTTT
Found at i:168433 original size:12 final size:12
Alignment explanation
Indices: 168416--168440 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
168406 GATAAAGAAA
168416 TAAAATTTTTAT
1 TAAAATTTTTAT
168428 TAAAATTTTTAT
1 TAAAATTTTTAT
168440 T
1 T
168441 TCCAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAAATTTTTAT
Found at i:168732 original size:18 final size:19
Alignment explanation
Indices: 168695--168732 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
168685 TTTTAAACTT
* *
168695 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
168714 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
168732 T
1 T
168733 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:168788 original size:17 final size:18
Alignment explanation
Indices: 168766--168800 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
168756 TATTATTGAA
168766 AATAACTTTTAT-AATTT
1 AATAACTTTTATCAATTT
168783 AATAACTTTTATCAATTT
1 AATAACTTTTATCAATTT
168801 TAATTTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAACTTTTATCAATTT
Found at i:170914 original size:2 final size:2
Alignment explanation
Indices: 170907--170939 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
170897 GGCCATTGAT
170907 TA TA TA 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 TA TA TA T
170940 GTCATTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:171841 original size:14 final size:14
Alignment explanation
Indices: 171826--171866 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
171816 CCTTATTGTT
171826 TTTTA-TTA-ATTA
1 TTTTATTTATATTA
171838 TTTTATTTATATTA
1 TTTTATTTATATTA
*
171852 TTTTGAATTATATTA
1 TTTT-ATTTATATTA
171867 GTTAACTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 5 0.20
13 3 0.12
14 8 0.32
15 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTATTTATATTA
Found at i:178432 original size:20 final size:20
Alignment explanation
Indices: 178401--178473 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
178391 TATATAAACG
*
178401 TGTCATAAAGGTAGAGAACA
1 TGTCACAAAGGTAGAGAACA
* *
178421 TGCCACAAAGGTAGATATAGACA
1 TGTCACAAAGGTAG--AGA-ACA
* *
178444 TGTCATAAAGGCAGAGAACA
1 TGTCACAAAGGTAGAGAACA
178464 TGTCACAAAG
1 TGTCACAAAG
178474 ACATAATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 24 0.57
21 2 0.05
22 2 0.05
23 14 0.33
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (20 bp):
TGTCACAAAGGTAGAGAACA
Found at i:178439 original size:43 final size:43
Alignment explanation
Indices: 178376--178473 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
178366 CAGATAAAAG
* * *
178376 CATGCCACAAAGGCATATATAAACGTGTCATAAAGGTAGAGAA
1 CATGCCACAAAGGCAGATATAAACATGTCATAAAGGCAGAGAA
* *
178419 CATGCCACAAAGGTAGATATAGACATGTCATAAAGGCAGAGAA
1 CATGCCACAAAGGCAGATATAAACATGTCATAAAGGCAGAGAA
*
178462 CATGTCACAAAG
1 CATGCCACAAAG
178474 ACATAATTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.17
Consensus pattern (43 bp):
CATGCCACAAAGGCAGATATAAACATGTCATAAAGGCAGAGAA
Found at i:178453 original size:23 final size:22
Alignment explanation
Indices: 178392--178454 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
178382 ACAAAGGCAT
*
178392 ATATAAACGTGTCATAAAGGTAG
1 ATAT-AACATGTCATAAAGGTAG
* * *
178415 --AGAACATGCCACAAAGGTAG
1 ATATAACATGTCATAAAGGTAG
178435 ATATAGACATGTCATAAAGG
1 ATATA-ACATGTCATAAAGG
178455 CAGAGAACAT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 2 0.07
23 12 0.40
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (22 bp):
ATATAACATGTCATAAAGGTAG
Found at i:187321 original size:65 final size:65
Alignment explanation
Indices: 187241--187393 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 65
187231 GCACTAAGGG
* * **
187241 TGTATCGATGCATAAAATGCATTCGATGTTT-TA-AACAAGCCTAGAGTGCATCTATGCATGGTC
1 TGTATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCCT-GAGTGCATCGATGCATGGAA
*
187304 TT
64 GT
*
187306 TGTATCGATGCATAAAATGCATTCGATGTTTCCATAAAATCCTGAGTGCATCGATGCATGGAAGT
1 TGTATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGAAGT
*
187371 T-CATCGATGCATAAAATGCATTC
1 TGTATCGATGCATAAAATGCATTC
187394 AAAATGGGGT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 21 0.27
65 50 0.63
66 6 0.08
67 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (65 bp):
TGTATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGAAGT
Found at i:195167 original size:66 final size:64
Alignment explanation
Indices: 195083--195239 Score: 212
Period size: 66 Copynumber: 2.4 Consensus size: 64
195073 TGGAACACTT
*
195083 AGTGCATCGATGCATAAAATGCATTCGATGTTT-TA-AACAAGCCTGGAGTGCATCGATGCATGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGCCT-GAGTGCATCGATGCATGG
*
195146 TT
64 -A
* * *
195148 TGTGCATCGAGTGCATAAAATGCATTCGATGTTTCCATGAAATCCTGAGTGCATCGATGCATGGA
1 AGTGCATCGA-TGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGA
195213 AGTGCATCGATGCAT-AAATGCATTCGA
1 AGTGCATCGATGCATAAAATGCATTCGA
195240 AATGGGGTGT
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
63 12 0.14
64 5 0.06
65 18 0.22
66 41 0.49
67 6 0.07
68 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGA
Found at i:205142 original size:21 final size:21
Alignment explanation
Indices: 205116--205174 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
205106 TCCTTAAGGA
*
205116 GTGGTCCTTCGGGACATCTAT
1 GTGGTCCTTCGGGACATATAT
205137 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
*
205158 GTGGTCATTCGGGACAT
1 GTGGTCCTTCGGGACAT
205175 TTCTACATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:205439 original size:9 final size:9
Alignment explanation
Indices: 205426--205460 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
205416 TTATATGAAT
205426 TAATGATAA
1 TAATGATAA
* *
205435 GAATGTTAA
1 TAATGATAA
205444 TAATGATAA
1 TAATGATAA
205453 TAATGATA
1 TAATGATA
205461 TGTGTTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (9 bp):
TAATGATAA
Found at i:207529 original size:18 final size:18
Alignment explanation
Indices: 207500--207635 Score: 102
Period size: 17 Copynumber: 7.8 Consensus size: 18
207490 ATTATAAATG
*
207500 TTTATAGTTATCAGATGA
1 TTTACAGTTATCAGATGA
* *
207518 TTTTCGGTTATCAGAT-A
1 TTTACAGTTATCAGATGA
*
207535 TTTACAGATATCAGATGA
1 TTTACAGTTATCAGATGA
* * *
207553 -TTACATTTATTATAT-A
1 TTTACAGTTATCAGATGA
*
207569 TTTACAGATATCAGATGA
1 TTTACAGTTATCAGATGA
*
207587 -TTACAGTTATCAAAT-A
1 TTTACAGTTATCAGATGA
** * * *
207603 TTTTTAGATATAAGATGT
1 TTTACAGTTATCAGATGA
*
207621 TTTACATTTATCAGA
1 TTTACAGTTATCAGA
207636 CACAGATTAA
Statistics
Matches: 86, Mismatches: 27, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
16 2 0.02
17 59 0.69
18 25 0.29
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:207575 original size:34 final size:34
Alignment explanation
Indices: 207525--207633 Score: 137
Period size: 34 Copynumber: 3.2 Consensus size: 34
207515 TGATTTTCGG
*
207525 TTATCAGATATTTACAGATATCAGATGATTACAT
1 TTATCAAATATTTACAGATATCAGATGATTACAT
* * *
207559 TTATTATATATTTACAGATATCAGATGATTACAG
1 TTATCAAATATTTACAGATATCAGATGATTACAT
** * *
207593 TTATCAAATATTTTTAGATATAAGATGTTTTACAT
1 TTATCAAATATTTACAGATATCAGATG-ATTACAT
207628 TTATCA
1 TTATCA
207634 GACACAGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
34 53 0.83
35 11 0.17
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (34 bp):
TTATCAAATATTTACAGATATCAGATGATTACAT
Found at i:209931 original size:23 final size:24
Alignment explanation
Indices: 209883--209928 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
209873 ATACCTGGTG
209883 TACCTAAAAATTATAAAAAATAAA
1 TACCTAAAAATTATAAAAAATAAA
209907 TACC-AAAAA-TA-AAATAAATAAA
1 TACCTAAAAATTATAAA-AAATAAA
209929 ATAAAATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.14
22 9 0.43
23 5 0.24
24 4 0.19
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (24 bp):
TACCTAAAAATTATAAAAAATAAA
Found at i:210738 original size:16 final size:16
Alignment explanation
Indices: 210717--210751 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
210707 TCAGTGTGCC
210717 AAACCTAGAAAAAATA
1 AAACCTAGAAAAAATA
210733 AAACCTAGAAAAAATA
1 AAACCTAGAAAAAATA
210749 AAA
1 AAA
210752 TCTTTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (16 bp):
AAACCTAGAAAAAATA
Found at i:215447 original size:19 final size:19
Alignment explanation
Indices: 215423--215485 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 19
215413 ATTTAAAATT
215423 AATAAA-AATAAATGAATAA
1 AATAAATAAT-AATGAATAA
*
215442 AATAAATAATATTGAAT-A
1 AATAAATAATAATGAATAA
**
215460 AA-AAATAATAATG-CGAA
1 AATAAATAATAATGAATAA
215477 AATAAATAA
1 AATAAATAA
215486 AATAGAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.35
18 9 0.24
19 12 0.32
20 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (19 bp):
AATAAATAATAATGAATAA
Found at i:215469 original size:20 final size:19
Alignment explanation
Indices: 215426--215471 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
215416 TAAAATTAAT
215426 AAAAATAA-A-TGAATAAA
1 AAAAATAATATTGAATAAA
*
215443 ATAAATAATATTGAATAAA
1 AAAAATAATATTGAATAAA
215462 AAATAATAAT
1 AAA-AATAAT
215472 GCGAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 10 0.42
20 6 0.25
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAAATAATATTGAATAAA
Found at i:216093 original size:13 final size:13
Alignment explanation
Indices: 216070--216104 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
216060 CTTAGCATTG
216070 TGAATAGAAAATAA
1 TGAA-AGAAAATAA
216084 TGAAAGAAAATAA
1 TGAAAGAAAATAA
*
216097 AGAAAGAA
1 TGAAAGAA
216105 TGAAAGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
TGAAAGAAAATAA
Found at i:217014 original size:21 final size:22
Alignment explanation
Indices: 216990--217041 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
216980 CCAAAATCTC
* * *
216990 AAACCATAAAAC-ATATATCCT
1 AAACCATAAAACTACAAAGCCT
*
217011 AAACC-TCAAACTACAAAGCCT
1 AAACCATAAAACTACAAAGCCT
217032 AAACCATAAA
1 AAACCATAAA
217042 CCTCAGTCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.17
Consensus pattern (22 bp):
AAACCATAAAACTACAAAGCCT
Found at i:217105 original size:14 final size:15
Alignment explanation
Indices: 217053--217106 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
217043 CTCAGTCCTT
*
217053 AAATTATAAACCCTA
1 AAATTCTAAACCCTA
* * *
217068 AATTTCTAAA-TCTT
1 AAATTCTAAACCCTA
217082 AAATTCTAAACCCTA
1 AAATTCTAAACCCTA
217097 AAATT-TAAAC
1 AAATTCTAAAC
217107 TTCAAATCTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTCTAAACCCTA
Found at i:217125 original size:21 final size:22
Alignment explanation
Indices: 217074--217125 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
217064 CCTAAATTTC
217074 TAAATCTTAAATTCTAAACCCT
1 TAAATCTTAAATTCTAAACCCT
* *
217096 AAAAT-TTAAACTTC-AAA-TCT
1 TAAATCTTAAA-TTCTAAACCCT
217116 TAAATCTTAA
1 TAAATCTTAA
217126 CCTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCTTAAATTCTAAACCCT
Found at i:221605 original size:30 final size:29
Alignment explanation
Indices: 221559--221694 Score: 114
Period size: 29 Copynumber: 4.6 Consensus size: 29
221549 AAACCCTAAA
*
221559 GGACTAAAATGGAAAAAATAGAAACTTAG
1 GGACTAAAATAGAAAAAATAGAAACTTAG
* * *
221588 GGACTAAAATAGTAAAAATAGAAAATTTTG
1 GGACTAAAATAGAAAAAATAG-AAACTTAG
* * *
221618 GGACCAAAAT-GAATAAAACAGAAACTTGAA
1 GGACTAAAATAGAA-AAAATAGAAACTT-AG
** *
221648 AAACTAAAATAGAAAAAATA-AAAATTAG
1 GGACTAAAATAGAAAAAATAGAAACTTAG
* *
221676 GTACAAAAATAGCAAAAAA
1 GGACTAAAATAG-AAAAAA
221695 CAAAAATTTA
Statistics
Matches: 83, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
28 10 0.12
29 37 0.45
30 33 0.40
31 3 0.04
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.18
Consensus pattern (29 bp):
GGACTAAAATAGAAAAAATAGAAACTTAG
Found at i:221641 original size:59 final size:59
Alignment explanation
Indices: 221559--221673 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
221549 AAACCCTAAA
* * *** *
221559 GGACTAAAATGGAAAAAATAGAAACTT-AGGGACTAAAATAGTAAAAATAGAAAATTTTG
1 GGACCAAAATGGAAAAAACAGAAACTTGAAAAACTAAAATAGAAAAAATA-AAAATTTTG
221618 GGACCAAAAT-GAATAAAACAGAAACTTGAAAAACTAAAATAGAAAAAATAAAAATT
1 GGACCAAAATGGAA-AAAACAGAAACTTGAAAAACTAAAATAGAAAAAATAAAAATT
221674 AGGTACAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 3 0.06
59 27 0.56
60 18 0.38
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (59 bp):
GGACCAAAATGGAAAAAACAGAAACTTGAAAAACTAAAATAGAAAAAATAAAAATTTTG
Found at i:221702 original size:29 final size:29
Alignment explanation
Indices: 221533--221748 Score: 100
Period size: 30 Copynumber: 7.3 Consensus size: 29
221523 TTGTATGACC
** * *
221533 AAAATAGCAAAAAACAAAACCCTAAAGGACT
1 AAAATAG-AAAAAACAAAA-ATTTAAGGACA
* * * * * *
221564 AAAATGGAAAAAATAGAAACTTAGGGACT
1 AAAATAGAAAAAACAAAAATTTAAGGACA
* * ** *
221593 AAAATAGTAAAAATAGAAAATTTTGGGACC
1 AAAATAGAAAAAACA-AAAATTTAAGGACA
* * ** *
221623 AAAAT-GAATAAAACAGAAACTTGAAAAACT
1 AAAATAGAA-AAAACA-AAAATTTAAGGACA
*
221653 AAAATAGAAAAAATAAAAA-TT-AGGTACA
1 AAAATAGAAAAAACAAAAATTTAAGG-ACA
221681 AAAATAGCAAAAAACAAAAATTTAAGGACA
1 AAAATAG-AAAAAACAAAAATTTAAGGACA
* * *
221711 AAAATA-TAAATACAGAAAATTATAAGG-CT
1 AAAATAGAAAAAACA-AAAATT-TAAGGACA
221740 AAAATAGAA
1 AAAATAGAA
221749 GTTACAAATA
Statistics
Matches: 143, Mismatches: 32, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 16 0.11
29 50 0.35
30 64 0.45
31 12 0.08
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.17
Consensus pattern (29 bp):
AAAATAGAAAAAACAAAAATTTAAGGACA
Found at i:221702 original size:88 final size:88
Alignment explanation
Indices: 221561--221728 Score: 207
Period size: 88 Copynumber: 1.9 Consensus size: 88
221551 ACCCTAAAGG
* * * * * ** *
221561 ACTAAAATGGAAAAAATAGAAACTTAGGGACTAAAATAGTAAAAATAGAAAATTTTGGGACCAAA
1 ACTAAAATAGAAAAAATAGAAAATTAGGGACAAAAATAGCAAAAATAAAAAATTTAAGGACAAAA
221626 ATGAATAAA-ACAGAAACTTGAAAA
66 AT--ATAAATACAGAAACTTGAAAA
*
221650 ACTAAAATAGAAAAAATA-AAAATTAGGTACAAAAATAGCAAAAA-ACAAAAATTTAAGGACAAA
1 ACTAAAATAGAAAAAATAGAAAATTAGGGACAAAAATAGCAAAAATA-AAAAATTTAAGGACAAA
221713 AATATAAATACAGAAA
65 AATATAAATACAGAAA
221729 ATTATAAGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 5 0.07
87 8 0.12
88 38 0.56
89 17 0.25
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.18
Consensus pattern (88 bp):
ACTAAAATAGAAAAAATAGAAAATTAGGGACAAAAATAGCAAAAATAAAAAATTTAAGGACAAAA
ATATAAATACAGAAACTTGAAAA
Found at i:221712 original size:30 final size:28
Alignment explanation
Indices: 221653--221716 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
221643 TTGAAAAACT
*
221653 AAAATAGAAAAAATAAAAATTAGGTACA
1 AAAATAGAAAAAACAAAAATTAGGTACA
221681 AAAATAGCAAAAAACAAAAATTTAAGG-ACA
1 AAAATAG-AAAAAACAAAAA-TT-AGGTACA
221711 AAAATA
1 AAAATA
221717 TAAATACAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.22
29 11 0.34
30 11 0.34
31 3 0.09
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.16
Consensus pattern (28 bp):
AAAATAGAAAAAACAAAAATTAGGTACA
Found at i:222207 original size:54 final size:54
Alignment explanation
Indices: 222125--222234 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
222115 TGAAACGGCG
222125 CCGTTTCATCACATGTATATATACCCAAAGCTTAGCCCAAACTTAAGCCATTCT
1 CCGTTTCATCACATGTATATATACCCAAAGCTTAGCCCAAACTTAAGCCATTCT
*
222179 CCGTTTCATCACATGTTTATATACCCAAAGCTTAGCCCAAACTTAAGCCATTCT
1 CCGTTTCATCACATGTATATATACCCAAAGCTTAGCCCAAACTTAAGCCATTCT
222233 CC
1 CC
222235 CATTTTTTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (54 bp):
CCGTTTCATCACATGTATATATACCCAAAGCTTAGCCCAAACTTAAGCCATTCT
Found at i:223025 original size:22 final size:22
Alignment explanation
Indices: 222974--223027 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
222964 CCGGGTCTCG
* * *
222974 GGTCTGGATCGGGTTGCATCTG
1 GGTCTGGTTCGGGTTGCAACTA
222996 GGTCTGGTTCGGGTTGCAACTA
1 GGTCTGGTTCGGGTTGCAACTA
223018 GGTCTGGTTC
1 GGTCTGGTTC
223028 ATTTCTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.19, G:0.39, T:0.33
Consensus pattern (22 bp):
GGTCTGGTTCGGGTTGCAACTA
Found at i:223103 original size:3 final size:3
Alignment explanation
Indices: 223095--223125 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
223085 ATGTAAAACA
223095 AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
223126 TTTTTTAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:223766 original size:126 final size:126
Alignment explanation
Indices: 223482--223770 Score: 375
Period size: 126 Copynumber: 2.3 Consensus size: 126
223472 ATCTCGTCAA
* * * * *
223482 GTGATGACACTGCTCATCTATTCATGAGTCTTAGACATCTAAAGGTGATAACACGGTTCCACTCT
1 GTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATATAAAGGTGATAACACGATTCCACTCT
* * * * * ** *
223547 ACTGAGGACGACTGGTTATATGAGTTGACACAGCTCCTACATAACGAGGAGATCTGATTAT
66 ACTGAGGACGACTGGTTATATAAGTTCACACAGCTCCTACAAAACAACGAGATCTGACCAG
* * *
223608 ATGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATATAAGGGTGATAATACGATTCCACTCT
1 GTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATATAAAGGTGATAACACGATTCCACTCT
* * *
223673 GA-T-AGGGACGACTGGTTATCTAAGTTCACACAGCTCCTACAAAATAACGAGATCTGGCCAG
66 -ACTGA-GGACGACTGGTTATATAAGTTCACACAGCTCCTACAAAACAACGAGATCTGACCAG
223734 GTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCA
1 GTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCA
223771 GGGGATTTTG
Statistics
Matches: 141, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
125 1 0.01
126 139 0.99
127 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (126 bp):
GTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCATATAAAGGTGATAACACGATTCCACTCT
ACTGAGGACGACTGGTTATATAAGTTCACACAGCTCCTACAAAACAACGAGATCTGACCAG
Found at i:228426 original size:34 final size:34
Alignment explanation
Indices: 228379--228462 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 34
228369 GGTTGTTCAA
* *
228379 ATAGTGCAATTTGGTTTGAACGGTGCAAAAAAAC
1 ATAGTGCAATTTGGTTAGAACGATGCAAAAAAAC
* * * *
228413 ATAGTGCAGTTTGGTTAGAACTATGCAGAAAAAT
1 ATAGTGCAATTTGGTTAGAACGATGCAAAAAAAC
*
228447 ACAGTGCAATTTGGTT
1 ATAGTGCAATTTGGTT
228463 CGAAATATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (34 bp):
ATAGTGCAATTTGGTTAGAACGATGCAAAAAAAC
Found at i:228477 original size:34 final size:34
Alignment explanation
Indices: 228381--228479 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 34
228371 TTGTTCAAAT
* *** * * *
228381 AGTGCAATTTGGTTTGAACGGTGCAAAAAAACAT
1 AGTGCAATTTGGTTAGAAATATGCAGAAAAATAC
* *
228415 AGTGCAGTTTGGTTAGAACTATGCAGAAAAATAC
1 AGTGCAATTTGGTTAGAAATATGCAGAAAAATAC
* *
228449 AGTGCAATTTGGTTCGAAATATGTAGAAAAA
1 AGTGCAATTTGGTTAGAAATATGCAGAAAAA
228480 ATTCACAGTG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.27
Consensus pattern (34 bp):
AGTGCAATTTGGTTAGAAATATGCAGAAAAATAC
Found at i:231326 original size:19 final size:19
Alignment explanation
Indices: 231302--231339 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
231292 TGATACATTT
231302 TTTAGATCTAGTCCTTGAA
1 TTTAGATCTAGTCCTTGAA
*
231321 TTTAGATTTAGTCCTTGAA
1 TTTAGATCTAGTCCTTGAA
231340 CTTTCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (19 bp):
TTTAGATCTAGTCCTTGAA
Found at i:231329 original size:28 final size:26
Alignment explanation
Indices: 231264--231329 Score: 60
Period size: 28 Copynumber: 2.3 Consensus size: 26
231254 TACAATTAGG
*
231264 TTTAGATCTTTTTAATTTAGTCCTAAA
1 TTTAGAT-TTTTTAATCTAGTCCTAAA
* *
231291 TTGATACATTTTTTAGATCTAGTCCTTGAA
1 TT--TAGATTTTTTA-ATCTAGTCC-TAAA
231321 TTTAGATTT
1 TTTAGATTT
231330 AGTCCTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
27 2 0.06
28 12 0.39
29 12 0.39
30 5 0.16
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (26 bp):
TTTAGATTTTTTAATCTAGTCCTAAA
Found at i:234582 original size:30 final size:32
Alignment explanation
Indices: 234521--234584 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
234511 TAGTTTTTTC
234521 GGGCTAAACTAGAACCTTTCCCTAGCTTTTACAA
1 GGGCTAAACTAGAACCTTTCCC-A-CTTTTACAA
*
234555 GGGCTAAGCTAGAACCTTT-CC-CTTTTACAA
1 GGGCTAAACTAGAACCTTTCCCACTTTTACAA
234585 AAGGATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.31
33 2 0.07
34 18 0.62
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (32 bp):
GGGCTAAACTAGAACCTTTCCCACTTTTACAA
Found at i:234949 original size:20 final size:20
Alignment explanation
Indices: 234924--234964 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
234914 CCGTTAGACA
234924 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
234944 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
234964 G
1 G
234965 ACATTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.39, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:236478 original size:19 final size:20
Alignment explanation
Indices: 236435--236482 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
236425 TCTAAATCCT
*
236435 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
236455 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
236474 TTTTCAAAA
1 TTTTCAAAA
236483 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:237409 original size:30 final size:32
Alignment explanation
Indices: 237350--237410 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 32
237340 GTTTTTTCGA
237350 GCTAAACTAGAACCTTTCCCTAGCTTTTACACGG
1 GCTAAACTAGAACCTTTCCC-A-CTTTTACACGG
*
237384 GCTAAGCTAGAACCTTT-CC-CTTTTACA
1 GCTAAACTAGAACCTTTCCCACTTTTACA
237411 AAACAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
33 2 0.08
34 16 0.62
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (32 bp):
GCTAAACTAGAACCTTTCCCACTTTTACACGG
Found at i:237776 original size:20 final size:20
Alignment explanation
Indices: 237751--237791 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
237741 CCGTTAGACA
237751 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
**
237771 GGGGGAATTTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
237791 G
1 G
237792 ACATTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.39, T:0.20
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:241058 original size:14 final size:14
Alignment explanation
Indices: 241039--241066 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
241029 GATCCATTAC
241039 TTGTATTTTAATAT
1 TTGTATTTTAATAT
241053 TTGTATTTTAATAT
1 TTGTATTTTAATAT
241067 AATTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTGTATTTTAATAT
Found at i:246037 original size:124 final size:128
Alignment explanation
Indices: 245885--246138 Score: 399
Period size: 131 Copynumber: 2.0 Consensus size: 128
245875 AACCCAAAAT
245885 CATAAAACCACCGAGCATAAAATCTTACA-CGATGACTTAAATAGAAAAT-AAAAATGATAAAAT
1 CATAAAACCACCGAGCATAAAATCTTACACCGATGACTTAAATAGAAAATAAAAAATGATAAAAT
* * * *
245948 GCAAGAAATCGT-A-TTTTTTTCGGATTGATTATGTCACGTAAAATAAAAACGAATCATATAC
66 GCAAGAAATCATAATTTTTTTTCGAATTAATTATGTCACATAAAATAAAAACGAATCATATAC
246009 CATAAAACCACCGAGCATAAAATCTTACACCGATGACTTAAATAGAAAATAAAAAAAATGATAAA
1 CATAAAACCACCGAGCATAAAATCTTACACCGATGACTTAAATAGAAAAT--AAAAAATGATAAA
* *
246074 ATGCAAGAAATCATAATTTTTTTTTCTAATTAATTATGTCACATAAAATAAAAACGTATCATATA
64 ATGCAAGAAATCATAA-TTTTTTTTCGAATTAATTATGTCACATAAAATAAAAACGAATCATATA
246139 GATCACGTTT
Statistics
Matches: 117, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
124 29 0.25
125 20 0.17
128 25 0.21
129 1 0.01
131 42 0.36
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (128 bp):
CATAAAACCACCGAGCATAAAATCTTACACCGATGACTTAAATAGAAAATAAAAAATGATAAAAT
GCAAGAAATCATAATTTTTTTTCGAATTAATTATGTCACATAAAATAAAAACGAATCATATAC
Found at i:248511 original size:17 final size:16
Alignment explanation
Indices: 248489--248522 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
248479 TGCTTAAATA
*
248489 AGAGTTTTTCTCGAAAG
1 AGAGTTTATCTC-AAAG
248506 AGAGTTTATCTCAAAG
1 AGAGTTTATCTCAAAG
248522 A
1 A
248523 AATGAAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (16 bp):
AGAGTTTATCTCAAAG
Found at i:250397 original size:2 final size:2
Alignment explanation
Indices: 250390--250431 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
250380 ATTTTCAATA
250390 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
250432 TGTGTGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251444 original size:76 final size:77
Alignment explanation
Indices: 251346--251501 Score: 176
Period size: 76 Copynumber: 2.0 Consensus size: 77
251336 CCCAATATAG
**
251346 TAAAAAACAATAAAAAAATGTAATTTTGATCACAACG-CTTTTAATGGATATTTAATTTGGAA-T
1 TAAAAAACAATAAAAAAATGTAATTCAGATCACAA-GTC-TTTAATGGATATTTAATTT-GAATT
251409 AACT-AATAAGAGTT
63 AACTAAATAAGAGTT
* * * * * * *
251423 TAAAAAAC-ATTAAAGAGTGTAATTCAGATTATAAGTCTTTAATTGATATTTAATTTGAATTAAT
1 TAAAAAACAATAAAAAAATGTAATTCAGATCACAAGTCTTTAATGGATATTTAATTTGAATTAAC
251487 TAAATAAGAGTT
66 TAAATAAGAGTT
251499 TAA
1 TAA
251502 TTAATTCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
74 3 0.04
75 23 0.34
76 33 0.49
77 8 0.12
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (77 bp):
TAAAAAACAATAAAAAAATGTAATTCAGATCACAAGTCTTTAATGGATATTTAATTTGAATTAAC
TAAATAAGAGTT
Found at i:262628 original size:18 final size:17
Alignment explanation
Indices: 262574--262622 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
262564 TTGGACTTTT
* *
262574 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
262592 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
262610 AGTGCATTCGATG
1 AGTGCA-TCGATG
262623 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:262659 original size:19 final size:19
Alignment explanation
Indices: 262639--262709 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
262629 AATAGCCAGA
*
262639 GTGCATCAATGCATGGC-G
1 GTGCATCGATGCATGGCTG
262657 AGTGCATCGATGCATGGCTG
1 -GTGCATCGATGCATGGCTG
262677 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
262696 GTGCATCGATGCAT
1 GTGCATCGATGCAT
262710 CAAATGCATT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 49 0.98
20 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:262830 original size:65 final size:65
Alignment explanation
Indices: 262675--262832 Score: 198
Period size: 65 Copynumber: 2.4 Consensus size: 65
262665 GATGCATGGC
*
262675 TGGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CT
262740 CA
64 CA
** * **
262742 --GTGCATCGATGCATGGTAAGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TC
1 TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
262803 A
65 A
262804 TGGTGCATCGATGCATGGATTGGTGCATC
1 TGGTGCATCGATGCATGG-TTGGTGCATC
262833 ACTCTGAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.27
65 52 0.66
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (65 bp):
TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCA
Done.