Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:221240 original size:12 final size:12
Alignment explanation
Indices: 221223--221247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
221213 TTTGATGCTT
221223 TCTCTTTGATTC
1 TCTCTTTGATTC
221235 TCTCTTTGATTC
1 TCTCTTTGATTC
221247 T
1 T
221248 AGTTGCTTGA
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:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTCTTTGATTC
Found at i:224198 original size:21 final size:21
Alignment explanation
Indices: 224172--224211 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
224162 CAGAACCCCA
*
224172 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
224193 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
224212 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:224244 original size:21 final size:21
Alignment explanation
Indices: 224193--224255 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
224183 ATTCCCCTGT
224193 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
224216 AGGAGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
224237 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
224256 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.57
22 3 0.09
23 12 0.34
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:230973 original size:13 final size:14
Alignment explanation
Indices: 230950--230979 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
230940 TTCTCATTAC
230950 AGACGTGCATATGA
1 AGACGTGCATATGA
230964 AGAC-TGCATATGA
1 AGACGTGCATATGA
230977 AGA
1 AGA
230980 TTGTTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:232124 original size:16 final size:17
Alignment explanation
Indices: 232103--232139 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
232093 AAAAACGTGA
232103 ATTTTTT-AGATTTTTT
1 ATTTTTTAAGATTTTTT
*
232119 ATTTTTTAATATTTTTT
1 ATTTTTTAAGATTTTTT
232136 ATTT
1 ATTT
232140 CCACGTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTTTTAAGATTTTTT
Found at i:237307 original size:19 final size:19
Alignment explanation
Indices: 237252--237307 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
237242 AGTCTCTAGG
*
237252 AGCACACGGCGACCTATAA
1 AGCACACGGCGACCTATGA
* *
237271 AGCACACGACAACCTATGA
1 AGCACACGGCGACCTATGA
**
237290 AGCACTTGGCGACCTATG
1 AGCACACGGCGACCTATG
237308 TTGCTGCAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.14
Consensus pattern (19 bp):
AGCACACGGCGACCTATGA
Found at i:246103 original size:45 final size:45
Alignment explanation
Indices: 246042--246135 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
246032 CCTTAGTATA
* *
246042 ATTTGTAAAACCAATATGATTGAATTAATAACATCCACATTGTGC
1 ATTTATAAAACCAATATGATTGAATGAATAACATCCACATTGTGC
* *
246087 ATTTATAAGACCAATATGATTGAATGAATAACATCCACGTTGTGC
1 ATTTATAAAACCAATATGATTGAATGAATAACATCCACATTGTGC
246132 ATTT
1 ATTT
246136 GTATAACTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (45 bp):
ATTTATAAAACCAATATGATTGAATGAATAACATCCACATTGTGC
Found at i:257592 original size:22 final size:22
Alignment explanation
Indices: 257566--257615 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
257556 GATGTTTCAA
257566 TTGTTTAAT-ATCAT-GTTATGAT
1 TTGTTTAATGAT-ATAGTTA-GAT
*
257588 TTGTTTACTGATATAGTTAGAT
1 TTGTTTAATGATATAGTTAGAT
257610 TTGTTT
1 TTGTTT
257616 GTATCTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (22 bp):
TTGTTTAATGATATAGTTAGAT
Found at i:259667 original size:22 final size:22
Alignment explanation
Indices: 259642--259683 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
259632 AAAAAGAATT
259642 AAAAATGAATA-AAATTTAATAC
1 AAAAAT-AATATAAATTTAATAC
259664 AAAAATAATATAAATTTAAT
1 AAAAATAATATAAATTTAAT
259684 TTTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAATAATATAAATTTAATAC
Found at i:259701 original size:26 final size:29
Alignment explanation
Indices: 259663--259717 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
259653 AAATTTAATA
*
259663 CAAAAATAATAT-AAATTTA-ATTTTTTT
1 CAAAAATAATATAAAATTTATAATTTTTT
259690 CAAAAAT-ATATAAAATTTATAATTTTTT
1 CAAAAATAATATAAAATTTATAATTTTTT
259718 AAATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 4 0.16
27 14 0.56
28 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (29 bp):
CAAAAATAATATAAAATTTATAATTTTTT
Found at i:261573 original size:10 final size:10
Alignment explanation
Indices: 261558--261596 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
261548 TTATCACACT
261558 AAATTCTCTC
1 AAATTCTCTC
261568 AAATTCTCT-
1 AAATTCTCTC
261577 AAATTTCTCTC
1 AAA-TTCTCTC
*
261588 AAATACTCT
1 AAATTCTCT
261597 TTTTTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:261586 original size:20 final size:19
Alignment explanation
Indices: 261556--261596 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
261546 TTTTATCACA
*
261556 CTAAATTCTCTCAAATTCT
1 CTAAATTCTCTCAAATACT
261575 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
261595 CT
1 CT
261597 TTTTTTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:261916 original size:111 final size:110
Alignment explanation
Indices: 261722--262028 Score: 533
Period size: 111 Copynumber: 2.8 Consensus size: 110
261712 TGGAAATCAT
* *
261722 ATATCTCTACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATAC-GTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
261787 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
261833 ATATCTCGATATTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATAC-GTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
261898 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
261944 TTATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACG-TAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
262009 TAATTAGTTGATTTATTTAA
65 TAATTAGTTGATTTATTTAA
262029 GAGAAAATAA
Statistics
Matches: 186, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
110 1 0.01
111 185 0.99
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (110 bp):
ATATCTCGACACTTTGCTGATACGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:262180 original size:20 final size:20
Alignment explanation
Indices: 262157--262212 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
262147 ATGTAAATCA
*
262157 CAATGCGATTATGACTATCG
1 CAATGCGATTCTGACTATCG
262177 CAATGCGATTCTGACTATCG
1 CAATGCGATTCTGACTATCG
*
262197 CAACGCGATTCTGACT
1 CAATGCGATTCTGACT
262213 GTCACAACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
CAATGCGATTCTGACTATCG
Found at i:262220 original size:20 final size:20
Alignment explanation
Indices: 262153--262220 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
262143 ATATATGTAA
* *
262153 ATCACAATGCGATTATGACT
1 ATCACAACGCGATTCTGACT
* *
262173 ATCGCAATGCGATTCTGACT
1 ATCACAACGCGATTCTGACT
*
262193 ATCGCAACGCGATTCTGACT
1 ATCACAACGCGATTCTGACT
*
262213 GTCACAAC
1 ATCACAAC
262221 ACTGAATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCACAACGCGATTCTGACT
Found at i:263077 original size:24 final size:23
Alignment explanation
Indices: 263040--263091 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
263030 GGTATTCGAA
*
263040 ATTTGATCTTGGTCAATACCCGG
1 ATTTTATCTTGGTCAATACCCGG
*
263063 ACTTTTATCTTGGTCAATACTCGG
1 A-TTTTATCTTGGTCAATACCCGG
263087 ATTTT
1 ATTTT
263092 GATGATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTTTATCTTGGTCAATACCCGG
Found at i:265360 original size:18 final size:18
Alignment explanation
Indices: 265337--265371 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
265327 AGAAAAAGGC
*
265337 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
265355 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
265372 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:265683 original size:140 final size:140
Alignment explanation
Indices: 265431--265700 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
265421 AAACGTTGTA
*
265431 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTAAACATTGCTA
* *
265496 TGATATGTTTAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
265561 TATGTATATT
131 TATGTATATT
*
265571 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTAAACATTGCTA
265636 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
265701 CGCAACGCGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTAAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTATATT
Found at i:265696 original size:20 final size:20
Alignment explanation
Indices: 265671--265782 Score: 119
Period size: 20 Copynumber: 5.9 Consensus size: 20
265661 TTACACATTC
*
265671 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
265691 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
265711 ATTTGATTATCGCATCTC-A
1 ATTTGACTATCGCAACGCGA
*
265730 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
265745 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
265765 ATATGACTATCGCAACGC
1 ATTTGACTATCGCAACGC
265783 AAAAATCGCA
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
14 8 0.11
15 3 0.04
19 3 0.04
20 61 0.81
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:265766 original size:54 final size:54
Alignment explanation
Indices: 265679--265800 Score: 199
Period size: 54 Copynumber: 2.3 Consensus size: 54
265669 TCATTTGAAT
* * * * *
265679 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCATCTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
265733 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
265787 ATCGCAACGCGAAT
1 ATCGCAACGCGAAT
265801 ATGTTGTCTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
Found at i:267046 original size:22 final size:22
Alignment explanation
Indices: 267019--267061 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
267009 GAGATATACG
267019 GATTTCGTCGGAGATGGGGACT
1 GATTTCGTCGGAGATGGGGACT
267041 GATTTCGTCGGAGATGGGGAC
1 GATTTCGTCGGAGATGGGGAC
267062 GGATGTCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.42, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACT
Found at i:267281 original size:20 final size:20
Alignment explanation
Indices: 267237--267310 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
267227 GCGCTTTGAA
*
267237 AATCGCATTGAGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
267257 CATCGCATTGCGACAGTTAG
1 AATCGCATTGCGATAGTCAG
** *
267277 AATCGTGTTGCTATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
267297 AATCGCGTTGCGAT
1 AATCGCATTGCGAT
267311 TGTCTTATTC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:270609 original size:51 final size:51
Alignment explanation
Indices: 270529--270663 Score: 155
Period size: 51 Copynumber: 2.6 Consensus size: 51
270519 CCCCTACGTG
* * *
270529 GCGTATAGCGCGG-AGCAGGGGGCATGCTATACTCCACGTGTAGCCCAATCA
1 GCGTATAGCGCGGTA-CAGGGGGCACGCTATACTCCACGTGGAGCCAAATCA
* * *
270580 GCGTATAGCGCGGTACAAGGGGCGCGCTATACTCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGTACAGGGGGCACGCTATACTCCACGTGGAGCCAAATCA
** * * *
270631 GTATATAGCGCGGTTCAGGGGGCATGCTTTACT
1 GCGTATAGCGCGGTACAGGGGGCACGCTATACT
270664 GCTACGGGTG
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
51 69 0.99
52 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.32, T:0.20
Consensus pattern (51 bp):
GCGTATAGCGCGGTACAGGGGGCACGCTATACTCCACGTGGAGCCAAATCA
Found at i:279545 original size:2 final size:2
Alignment explanation
Indices: 279538--279571 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
279528 ATTACATTTA
279538 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
279572 TATTACGAAT
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:279820 original size:31 final size:31
Alignment explanation
Indices: 279784--279842 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
279774 AACTTGAAAG
* * *
279784 AGTTTTGCAATAGTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
279815 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
279843 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:279878 original size:21 final size:22
Alignment explanation
Indices: 279854--279904 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
279844 CATACAACTA
279854 AAAT-AATAAAT-TATTTAAAAT
1 AAATCAATAAATAT-TTTAAAAT
**
279875 AAATCAATCTATATTTTAAAAT
1 AAATCAATAAATATTTTAAAAT
279897 AAATCAAT
1 AAATCAAT
279905 CTATTCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATCAATAAATATTTTAAAAT
Found at i:279892 original size:22 final size:22
Alignment explanation
Indices: 279867--279908 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
279857 TAATAAATTA
279867 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
279889 TTTAAAATAAATCAATCTAT
1 TTTAAAATAAATCAATCTAT
279909 TCTAATAAAT
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:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:279918 original size:22 final size:22
Alignment explanation
Indices: 279870--279918 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
279860 TAAATTATTT
* *
279870 AAAATAAATCAATCTATATTTT
1 AAAATAAATCAATCTATATCTA
279892 AAAATAAATCAATCTAT-TCTA
1 AAAATAAATCAATCTATATCTA
279913 ATAAAT
1 A-AAAT
279919 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAATCAATCTATATCTA
Found at i:279927 original size:32 final size:31
Alignment explanation
Indices: 279889--280222 Score: 326
Period size: 32 Copynumber: 11.7 Consensus size: 31
279879 CAATCTATAT
*
279889 TTTAAAATAAATCAATCTATTCTAATAAATTA
1 TTTAAAATAAATCAATC-ATACTAATAAATTA
279921 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
279953 TTTAAAATAAATCAAT--T-C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
279975 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
280007 TTTAAAATAAATCAATC---C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
280029 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
280061 TTTAAAATAAATCAATC---C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
280083 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAA-TCATACTAATAAATTA
280115 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
280147 TTTAAAATAAATCAATC---C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
280169 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
*
280201 TTTAAAACAAATCAATCCATAC
1 TTTAAAATAAATCAAT-CATAC
280223 AACTACAATA
Statistics
Matches: 258, Mismatches: 2, Indels: 84
0.75 0.01 0.24
Matches are distributed among these distances:
22 63 0.24
23 8 0.03
24 4 0.02
25 1 0.00
26 12 0.05
28 12 0.05
29 1 0.00
30 4 0.02
31 8 0.03
32 144 0.56
33 1 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATCATACTAATAAATTA
Found at i:279955 original size:86 final size:85
Alignment explanation
Indices: 279857--280463 Score: 571
Period size: 86 Copynumber: 7.3 Consensus size: 85
279847 ACAACTAAAA
*
279857 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATTCTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATC-ATACTAATAAATTAT
279922 TTAAAATAAATCAATCCATAC
65 TTAAAATAAATCAATCCATAC
279943 TAATAAATTATTTAAAATAAATCAAT-TCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 TAATAAATTATTTAAAATAAATCAATCT-ATATTTTAAAATAAATCAAT-CATACTAATAAATTA
280007 TTTAAAATAAATCAATCCATA-
64 TTTAAAATAAATCAATCCATAC
** * *
280028 TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC---C--AT--
1 TAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCATACTAATAA
*
280081 A-T-TTTAAAATAAATCAATTCATAC
60 ATTATTTAAAATAAATCAATCCATAC
* * * * * * * * **
280105 TAATAAATTATTTAAAATAAATCAATCCATA-CTAATAAATTATTTAA-AATAAATCAATCCA-T
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTA-AAATAAATCAATCAT-ACT-AATAAATT
280167 ATTTTAAAATAAATCAATCCATAC
63 A-TTTAAAATAAATCAATCCATAC
* * *** * *
280191 TAATAAATTATTTAAAACAAATCAATCCATACAACTACAAT-AAT-AA--AT-C-AATCAA-TAT
1 TAATAAATTATTTAAAATAAATCAATCTATA-TTTTAAAATAAATCAATCATACTAATAAATTA-
280249 TTTAAAATAAATCAATCCATAC
64 TTTAAAATAAATCAATCCATAC
* *
280271 TAATAAATTATTTAAAATTAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAAT-CATACTAATAAATTAT
280336 TTAAAATAAATCAATCCATAC
65 TTAAAATAAATCAATCCATAC
*
280357 -AACTACA--A--T--AATAAATCAAT-TCATATTTTAAAATAAATCAATTCATACTAATAAATT
1 TAA-TAAATTATTTAAAATAAATCAATCT-ATATTTTAAAATAAATCAA-TCATACTAATAAATT
280414 ATTTAAAATAAATCAATCCATAC
63 ATTTAAAATAAATCAATCCATAC
280437 TAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
280464 CATACTAATA
Statistics
Matches: 435, Mismatches: 39, Indels: 93
0.77 0.07 0.16
Matches are distributed among these distances:
75 2 0.00
76 28 0.06
77 6 0.01
78 2 0.00
79 6 0.01
80 145 0.33
81 8 0.02
82 18 0.04
83 1 0.00
84 9 0.02
85 13 0.03
86 190 0.44
87 6 0.01
88 1 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (85 bp):
TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCATACTAATAAATTATT
TAAAATAAATCAATCCATAC
Found at i:279979 original size:22 final size:22
Alignment explanation
Indices: 279953--279995 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
279943 TAATAAATTA
*
279953 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
279975 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
279996 CTAATAAATT
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:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:279979 original size:54 final size:54
Alignment explanation
Indices: 279921--280467 Score: 547
Period size: 54 Copynumber: 10.0 Consensus size: 54
279911 TAATAAATTA
*
279921 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
279975 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
280029 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
280083 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * ** * ** **
280138 AATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACT
1 TTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCATA-T
** * * * * * *
280192 AATAAATTATTTAAAACAAATCAAT-C-CATACAACTA--CAATAATAAATCAATCAATAT
1 TTTAAA--A--TAAATC-AATCCATACTAATA-AATTATTTAA-AATAAATCAATCCATAT
*
280249 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATTAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
280303 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * ** * ** * ** **
280360 TACAATAATAAATCAATTCATA-TTTTAAAATAAAT-CAATTCATACTAATAAAT-T
1 TTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
280414 ATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
280468 CTAATAAATT
Statistics
Matches: 407, Mismatches: 61, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
52 6 0.01
53 12 0.03
54 281 0.69
55 24 0.06
56 15 0.04
57 20 0.05
58 46 0.11
59 1 0.00
60 2 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:280004 original size:22 final size:22
Alignment explanation
Indices: 279955--280003 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
279945 ATAAATTATT
* **
279955 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
279977 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
280000 TAAA
1 TAAA
280004 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:280033 original size:22 final size:22
Alignment explanation
Indices: 280007--280049 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
279997 TAATAAATTA
280007 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
280029 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
280050 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:280058 original size:22 final size:22
Alignment explanation
Indices: 280009--280057 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
279999 ATAAATTATT
**
280009 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
280031 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
280054 TAAA
1 TAAA
280058 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:280087 original size:22 final size:22
Alignment explanation
Indices: 280061--280103 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
280051 TAATAAATTA
280061 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
280083 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
280104 CTAATAAATT
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:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:280112 original size:22 final size:22
Alignment explanation
Indices: 280063--280111 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
280053 ATAAATTATT
**
280063 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
280085 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
280108 TAAA
1 TAAA
280112 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:280173 original size:22 final size:22
Alignment explanation
Indices: 280147--280189 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
280137 TAATAAATTA
280147 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
280169 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
280190 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:280198 original size:22 final size:22
Alignment explanation
Indices: 280149--280197 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
280139 ATAAATTATT
**
280149 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
280171 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
280194 TAAA
1 TAAA
280198 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:280288 original size:32 final size:32
Alignment explanation
Indices: 280249--280356 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
280239 CAATCAATAT
280249 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
280281 TTTAAAATTAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
280303 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
280335 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
280357 AACTACAATA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
22 15 0.23
23 2 0.03
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.03
32 37 0.58
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:280307 original size:22 final size:22
Alignment explanation
Indices: 280281--280323 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
280271 TAATAAATTA
*
280281 TTTAAAATTAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
280303 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
280324 CTAATAAATT
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:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:280332 original size:22 final size:22
Alignment explanation
Indices: 280283--280331 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
280273 ATAAATTATT
* **
280283 TAAAATTAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
280305 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
280328 TAAA
1 TAAA
280332 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:280409 original size:18 final size:18
Alignment explanation
Indices: 280365--280476 Score: 69
Period size: 18 Copynumber: 6.4 Consensus size: 18
280355 ACAACTACAA
*
280365 TAATAAATCAATTCATATTT
1 TAATAAATCAATTCATA--C
280385 TAAAATAAATCAATTCATAC
1 T--AATAAATCAATTCATAC
*
280405 TAATAAAT-TATT--TA-
1 TAATAAATCAATTCATAC
* *
280419 AAATAAATCAATCCATAC
1 TAATAAATCAATTCATAC
*
280437 TAATAAAT-TATT--TA-
1 TAATAAATCAATTCATAC
* *
280451 AAATAAATCAATCCATAC
1 TAATAAATCAATTCATAC
280469 TAATAAAT
1 TAATAAAT
280477 TATTTAAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
14 14 0.20
15 8 0.11
17 9 0.13
18 21 0.30
20 2 0.03
22 16 0.23
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAAATCAATTCATAC
Found at i:280412 original size:22 final size:22
Alignment explanation
Indices: 280337--280411 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
280327 ATAAATTATT
* *
280337 TAAAATAAATCAATCCATACAA
1 TAAAATAAATCAATTCATATAA
**
280359 CTACAATAATAAATCAATTCATATTT
1 -T--AA-AATAAATCAATTCATATAA
280385 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
280408 TAAA
1 TAAA
280412 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:280525 original size:15 final size:15
Alignment explanation
Indices: 280499--280618 Score: 186
Period size: 15 Copynumber: 8.0 Consensus size: 15
280489 AATCAATCCA
*
280499 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
280514 TAATTTAAAATAAAT
1 TATTTTAAAATAAAT
*
280529 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
280544 TAATTTAAAATAAAT
1 TATTTTAAAATAAAT
*
280559 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
280574 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
280589 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
280604 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
280619 AACCTTATTA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 94 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:280535 original size:30 final size:30
Alignment explanation
Indices: 280499--280618 Score: 222
Period size: 30 Copynumber: 4.0 Consensus size: 30
280489 AATCAATCCA
280499 TATTTTATAATAAATTAATTTAAAATAAAT
1 TATTTTATAATAAATTAATTTAAAATAAAT
280529 TATTTTATAATAAATTAATTTAAAATAAAT
1 TATTTTATAATAAATTAATTTAAAATAAAT
*
280559 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTAATTTAAAATAAAT
*
280589 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTAATTTAAAATAAAT
280619 AACCTTATTA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTTTATAATAAATTAATTTAAAATAAAT
Found at i:287968 original size:31 final size:33
Alignment explanation
Indices: 287896--287990 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 33
287886 AGTGGACGGA
287896 AGGAAGCATCGGCACTTTCGATTCAAGAAGAAC
1 AGGAAGCATCGGCACTTTCGATTCAAGAAGAAC
*
287929 GAAAGGAAGCATCGGCACTTTCGATTCAAG-TGAAC
1 ---AGGAAGCATCGGCACTTTCGATTCAAGAAGAAC
* *
287964 GGAAGGAAGCGTCAGCACTTTCGATTC
1 ---AGGAAGCATCGGCACTTTCGATTC
287991 GATTGTTCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
35 28 0.51
36 27 0.49
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (33 bp):
AGGAAGCATCGGCACTTTCGATTCAAGAAGAAC
Found at i:287971 original size:35 final size:35
Alignment explanation
Indices: 287853--287990 Score: 177
Period size: 36 Copynumber: 3.9 Consensus size: 35
287843 TGAATAAGAA
* *
287853 GAACGAAAGGAAGCATTAGTACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC-AAGT
* * * *
287889 GGACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAG-T
*
287925 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
287960 GAACGGAAGGAAGCGTCAGCACTTTCGATTC
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC
287991 GATTGTTCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
35 31 0.35
36 58 0.65
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:289474 original size:21 final size:20
Alignment explanation
Indices: 289447--289545 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
289437 AATTAGTTTC
289447 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
289468 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
289489 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
289509 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
289530 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
289546 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 17 0.29
21 42 0.71
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:289538 original size:20 final size:20
Alignment explanation
Indices: 289513--289823 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
289503 GATTTTCAAT
* *
289513 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
289533 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
289553 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
289573 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
289593 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
289613 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
289633 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
289653 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
289674 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
289694 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
289714 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
289734 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
289754 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
289774 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
289794 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
289814 AATCGCAACG
1 AATCGCAACG
289824 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:289558 original size:40 final size:40
Alignment explanation
Indices: 289513--289902 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
289503 GATTTTCAAT
* ** * * *
289513 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
289553 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
289593 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
289633 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
289674 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
289714 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
289754 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
289794 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
289834 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
289874 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
289903 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:289830 original size:20 final size:19
Alignment explanation
Indices: 289551--289902 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
289541 CGCGAACACA
289551 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
289571 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
289591 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
289611 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
289631 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
289651 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
289671 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
289692 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
289712 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
289732 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
289752 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
289772 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
289792 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
289812 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
289832 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
289852 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
289872 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
289892 TAAATCACAAC
1 TAAATCGCAAC
289903 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:290617 original size:24 final size:24
Alignment explanation
Indices: 290578--290624 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
290568 AAATTTGGTC
290578 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
290602 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
290625 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:290816 original size:12 final size:12
Alignment explanation
Indices: 290799--290823 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
290789 ATATAATCCT
290799 GAAGAAGAAAAA
1 GAAGAAGAAAAA
290811 GAAGAAGAAAAA
1 GAAGAAGAAAAA
290823 G
1 G
290824 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:293196 original size:19 final size:19
Alignment explanation
Indices: 293133--293378 Score: 342
Period size: 19 Copynumber: 13.7 Consensus size: 19
293123 AAATCCCAAC
293133 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
293153 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
293168 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
293186 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
293205 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
293220 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
293238 ATGAAAATCGCAATGTGAA
1 ATGAAAATCGCAATGCGAA
293257 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
293276 ATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
293295 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
293314 ATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAA
293331 A-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
293347 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
293366 ATGAAAATCGCAA
1 ATGAAAATCGCAA
293379 CGAGATAATC
Statistics
Matches: 203, Mismatches: 8, Indels: 31
0.84 0.03 0.13
Matches are distributed among these distances:
14 28 0.14
15 2 0.01
16 10 0.05
17 9 0.04
18 3 0.01
19 138 0.68
20 13 0.06
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:293300 original size:109 final size:105
Alignment explanation
Indices: 293133--293400 Score: 450
Period size: 109 Copynumber: 2.5 Consensus size: 105
293123 AAATCCCAAC
293133 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
293197 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
* *
293238 ATGAAAATCGCAATGTGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
293303 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
293347 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
293401 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 32 0.21
105 15 0.10
106 4 0.03
107 5 0.03
108 1 0.01
109 96 0.63
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:293416 original size:52 final size:52
Alignment explanation
Indices: 293133--293400 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
293123 AAATCCCAAC
293133 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
293186 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
293238 ATGAAAATCGCAATGTGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
293295 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
293347 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
293399 AT
1 AT
293401 TATAAACGCA
Statistics
Matches: 205, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 133 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 45 0.22
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:293497 original size:19 final size:19
Alignment explanation
Indices: 293407--293489 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
293397 AAATTATAAA
293407 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
293426 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
293446 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
293462 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
293479 CGCATTGCGAT
1 CGCATTGCGAT
293490 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:293615 original size:14 final size:14
Alignment explanation
Indices: 293596--293632 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
293586 CATCAATTAC
293596 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
293610 ACAAATCATCTTTT
1 ACAAATCAACTTTT
293624 ACAAATCAA
1 ACAAATCAA
293633 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:295604 original size:14 final size:14
Alignment explanation
Indices: 295585--295641 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
295575 GCGAAATGAA
*
295585 AATCGCAACGACAG
1 AATCGCAACGAAAG
295599 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
295616 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
295632 AATCGCAACG
1 AATCGCAACG
295642 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:295612 original size:33 final size:33
Alignment explanation
Indices: 295566--295658 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
295556 GCGAAACCAA
*
295566 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
295599 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
295632 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
295659 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:295623 original size:19 final size:19
Alignment explanation
Indices: 295529--295663 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
295519 TAGTTTACTT
* *
295529 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
295549 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
295568 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
295587 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
295601 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
295620 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
295634 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
295653 TCGCAATGCGA
1 TCGCAACGCGA
295664 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:295681 original size:19 final size:19
Alignment explanation
Indices: 295659--295787 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
295649 AAAATCGCAA
295659 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
295678 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
295692 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
295711 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
295725 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
295744 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
295763 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
295783 TGCGA
1 TGCGA
295788 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:295701 original size:33 final size:33
Alignment explanation
Indices: 295659--295750 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
295649 AAAATCGCAA
295659 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
295692 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
295725 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
295751 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:296000 original size:92 final size:93
Alignment explanation
Indices: 295831--296208 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
295821 TTGAATGGAT
295831 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
295896 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
295924 AAATTTACTTTCAACCAAAAGAAAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
295988 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
296016 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
296079 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
296107 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
296172 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
296200 AAATTTACT
1 AAATTTACT
296209 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 89 0.32
92 95 0.34
93 96 0.34
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:297933 original size:14 final size:14
Alignment explanation
Indices: 297914--298003 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
297904 TTGAAATGAA
297914 AATCGCAACGAGAG
1 AATCGCAACGAGAG
297928 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
297945 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
297961 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
297980 AATCGCAACGAGAG
1 AATCGCAACGAGAG
297994 AATCGCAACG
1 AATCGCAACG
298004 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:297951 original size:33 final size:33
Alignment explanation
Indices: 297906--298020 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
297896 TCTTTTGGTT
297906 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
297939 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
297972 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
298005 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
298021 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:297952 original size:19 final size:18
Alignment explanation
Indices: 297913--298025 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
297903 GTTGAAATGA
297913 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
297928 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
297945 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
297961 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
297978 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
297994 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
298011 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
298026 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:298056 original size:14 final size:14
Alignment explanation
Indices: 298037--298091 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
298027 TTTGGTTTCG
298037 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
298051 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
298070 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
298084 CGTTGCGA
1 CGTTGCGA
298092 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:298069 original size:33 final size:33
Alignment explanation
Indices: 298021--298091 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
298011 AAAATCGCAA
**
298021 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
298054 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
298087 TGCGA
1 TGCGA
298092 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:298099 original size:33 final size:33
Alignment explanation
Indices: 298032--298113 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
298022 GCGATTTTGG
***
298032 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
298065 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
298098 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
298114 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:298118 original size:20 final size:20
Alignment explanation
Indices: 298044--298132 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
298034 TCGCGTTGCG
298044 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
298064 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
298077 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
298097 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
298117 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
298133 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:298256 original size:33 final size:33
Alignment explanation
Indices: 298214--298278 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
298204 TACTAACTTG
*
298214 AAAATCGCAACGAGAGAATAGCAACGCGAAATA
1 AAAATCGCAACGACAGAATAGCAACGCGAAATA
* *
298247 AAAATCGCAACGACAGAATCGTAACGCGAAAT
1 AAAATCGCAACGACAGAATAGCAACGCGAAAT
298279 GAAATCTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATAGCAACGCGAAATA
Found at i:298515 original size:22 final size:22
Alignment explanation
Indices: 298463--298517 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
298453 TGGTTGTGAG
**
298463 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
298485 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
298507 GGATTTCTTCG
1 GGATTTCTTCG
298518 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:298688 original size:20 final size:20
Alignment explanation
Indices: 298663--298855 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
298653 CTTTAAATAT
298663 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
298683 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
298705 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
298724 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
298744 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
298764 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
298784 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
298804 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
298824 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
298844 CGCGTTGCGATT
1 CGCGTTGCGATT
298856 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:298850 original size:60 final size:60
Alignment explanation
Indices: 298663--298855 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
298653 CTTTAAATAT
**
298663 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
298724 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
298784 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
298844 CGCGTTGCGATT
1 CGCGTTGCGATT
298856 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:302125 original size:43 final size:43
Alignment explanation
Indices: 302064--302149 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
302054 TACTAATGTG
302064 CAATTGTACATGGAAGTAATGAAATAATGATGATCATCTGATC
1 CAATTGTACATGGAAGTAATGAAATAATGATGATCATCTGATC
302107 CAATTGTACATGGAAGTAATGAAATAATGATGATCATCTGATC
1 CAATTGTACATGGAAGTAATGAAATAATGATGATCATCTGATC
302150 GTATGATGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (43 bp):
CAATTGTACATGGAAGTAATGAAATAATGATGATCATCTGATC
Found at i:302364 original size:22 final size:23
Alignment explanation
Indices: 302339--302387 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
302329 AACCAAAATC
302339 AACCAG-AACTGAAATTAACCCG
1 AACCAGAAACTGAAATTAACCCG
302361 AACC-GAAACTGAAATTAACCCG
1 AACCAGAAACTGAAATTAACCCG
302383 AACCA
1 AACCA
302388 AAATTAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.47, C:0.29, G:0.12, T:0.12
Consensus pattern (23 bp):
AACCAGAAACTGAAATTAACCCG
Found at i:302380 original size:16 final size:16
Alignment explanation
Indices: 302367--302417 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
302357 CCCGAACCGA
302367 AACTGAAATTAACCCG
1 AACTGAAATTAACCCG
**
302383 AACCAAAATTAACCCG
1 AACTGAAATTAACCCG
*
302399 AACTGAAATTGACCCG
1 AACTGAAATTAACCCG
302415 AAC
1 AAC
302418 CGAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.16
Consensus pattern (16 bp):
AACTGAAATTAACCCG
Found at i:302403 original size:32 final size:32
Alignment explanation
Indices: 302367--302512 Score: 131
Period size: 32 Copynumber: 4.6 Consensus size: 32
302357 CCCGAACCGA
** *
302367 AACTGAAATTAACCCGAACCAAAATTAACCCG
1 AACTGAAAGCAACCCGAACCAAATTTAACCCG
*** *
302399 AACTGAAATTGACCCGAACCGAATTTAAACCC-
1 AACTGAAAGCAACCCGAACCAAATTT-AACCCG
* *
302431 AATCAT-AAAGCAATCCGAACCAAATTTATCCCG
1 AA-C-TGAAAGCAACCCGAACCAAATTTAACCCG
302464 -ACTCGAAAGCAACCC-AACCAAATTTAACCCG
1 AACT-GAAAGCAACCCGAACCAAATTTAACCCG
302495 -ACTCGAAAGCAACCCGAA
1 AACT-GAAAGCAACCCGAA
302513 TAGATTGAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
30 1 0.01
31 31 0.32
32 41 0.43
33 22 0.23
34 1 0.01
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.16
Consensus pattern (32 bp):
AACTGAAAGCAACCCGAACCAAATTTAACCCG
Found at i:302485 original size:31 final size:31
Alignment explanation
Indices: 302437--302509 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
302427 ACCCAATCAT
* *
302437 AAAGCAATCCGAACCAAATTTATCCCGACTCG
1 AAAGCAA-CCCAACCAAATTTAACCCGACTCG
302469 AAAGCAACCCAACCAAATTTAACCCGACTCG
1 AAAGCAACCCAACCAAATTTAACCCGACTCG
302500 AAAGCAACCC
1 AAAGCAACCC
302510 GAATAGATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 32 0.82
32 7 0.18
ACGTcount: A:0.41, C:0.34, G:0.11, T:0.14
Consensus pattern (31 bp):
AAAGCAACCCAACCAAATTTAACCCGACTCG
Found at i:302510 original size:16 final size:16
Alignment explanation
Indices: 302460--302511 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
302450 CCAAATTTAT
302460 CCCGACTCGAAAGCAA
1 CCCGACTCGAAAGCAA
* **
302476 CCCAAC-C-AAATTTAA
1 CCCGACTCGAAA-GCAA
302491 CCCGACTCGAAAGCAA
1 CCCGACTCGAAAGCAA
302507 CCCGA
1 CCCGA
302512 ATAGATTGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 3 0.11
15 8 0.30
16 13 0.48
17 3 0.11
ACGTcount: A:0.38, C:0.38, G:0.13, T:0.10
Consensus pattern (16 bp):
CCCGACTCGAAAGCAA
Found at i:303279 original size:32 final size:32
Alignment explanation
Indices: 303208--303281 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
303198 AGGTTGACCT
* * *
303208 AAACCGAAAATCAACCGATTCGGTATTAACCC
1 AAACCAAAAATCAACCGATCCGATATTAACCC
* * * *
303240 AATCCAAAAATCAACTGATCCGATATTGATCC
1 AAACCAAAAATCAACCGATCCGATATTAACCC
303272 AAACCAAAAA
1 AAACCAAAAA
303282 ATAATCGATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.19
Consensus pattern (32 bp):
AAACCAAAAATCAACCGATCCGATATTAACCC
Found at i:303856 original size:28 final size:29
Alignment explanation
Indices: 303805--303863 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
303795 TATAATCACC
303805 TTAATTTAATAAAAAAATATATTTAAAAA
1 TTAATTTAATAAAAAAATATATTTAAAAA
*
303834 TTAATTTAATAAAAAAA-ATATTTAACAA
1 TTAATTTAATAAAAAAATATATTTAAAAA
303862 TT
1 TT
303864 GTGACTTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TTAATTTAATAAAAAAATATATTTAAAAA
Found at i:311513 original size:30 final size:30
Alignment explanation
Indices: 311476--311564 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
311466 TAAAATATAT
*
311476 AACTTTTTAAAATTACATTTTTAGCCCCTA
1 AACTTTTTAAAATTACATTTTTAGCCACTA
* * *
311506 TACTTTTTAAAGTT-TATATTTTAGCCACTA
1 AACTTTTTAAAATTACAT-TTTTAGCCACTA
* *
311536 AAC-TTTCAAAACTTACA-TTTTAGACACTA
1 AACTTTTTAAAA-TTACATTTTTAGCCACTA
311565 GTTTGGGGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
29 19 0.40
30 27 0.57
31 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (30 bp):
AACTTTTTAAAATTACATTTTTAGCCACTA
Found at i:312247 original size:2 final size:2
Alignment explanation
Indices: 312240--312293 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
312230 ATTTTGGAAT
312240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
312282 TA TA TA TA TA TA
1 TA TA TA TA TA TA
312294 CAATTGAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:327910 original size:21 final size:20
Alignment explanation
Indices: 327886--327934 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
327876 TTTTTGTTCC
* *
327886 GTTTTGATCATTCAATTTTTT
1 GTTTTGATCATT-AATGTTTA
**
327907 GTTTAAATCATTAATGTTTA
1 GTTTTGATCATTAATGTTTA
327927 GTTTTGAT
1 GTTTTGAT
327935 TTTATTTTGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.57
Consensus pattern (20 bp):
GTTTTGATCATTAATGTTTA
Found at i:329373 original size:14 final size:13
Alignment explanation
Indices: 329340--329378 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
329330 CGTGTTTTGG
329340 TAATTAAAAAAT-
1 TAATTAAAAAATA
*
329352 TAAATAAAAAATA
1 TAATTAAAAAATA
329365 TATATTAAAAAATA
1 TA-ATTAAAAAATA
329379 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATTAAAAAATA
Found at i:331257 original size:14 final size:14
Alignment explanation
Indices: 331240--331299 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
331230 AATATGTTTG
331240 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
* *
331254 TTTATGTTTGTTCG
1 TTTATGTTCGTTCA
331268 TTTATGTTC--T--
1 TTTATGTTCGTTCA
*
331278 TTTATGTGCGTTCA
1 TTTATGTTCGTTCA
331292 TTTATGTT
1 TTTATGTT
331300 TAGCCTAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 8 0.22
12 2 0.05
14 27 0.73
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:331276 original size:24 final size:24
Alignment explanation
Indices: 331249--331299 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
331239 GTTTATGTTC
** *
331249 GTTCATTTATGTTTGTTCGTTTAT
1 GTTCATTTATGTGCGTTCATTTAT
*
331273 GTTCTTTTATGTGCGTTCATTTAT
1 GTTCATTTATGTGCGTTCATTTAT
331297 GTT
1 GTT
331300 TAGCCTAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (24 bp):
GTTCATTTATGTGCGTTCATTTAT
Found at i:331514 original size:14 final size:14
Alignment explanation
Indices: 331495--331531 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
331485 GTTAGTTTAT
331495 GTTCGTTTACATCC
1 GTTCGTTTACATCC
331509 GTTCGTTTACATCC
1 GTTCGTTTACATCC
331523 GTTCGTTTA
1 GTTCGTTTA
331532 TGTTCGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (14 bp):
GTTCGTTTACATCC
Found at i:338708 original size:6 final size:7
Alignment explanation
Indices: 338682--338706 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
338672 CACAGCTTAG
338682 TTTTTCT
1 TTTTTCT
338689 TTTTTCT
1 TTTTTCT
338696 TTTTTCT
1 TTTTTCT
338703 TTTT
1 TTTT
338707 CTAAGTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:340575 original size:7 final size:7
Alignment explanation
Indices: 340563--340589 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
340553 ATCCCTATGC
340563 ATATATA
1 ATATATA
340570 ATATATA
1 ATATATA
340577 ATATATA
1 ATATATA
340584 ATATAT
1 ATATAT
340590 GCATATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:347038 original size:16 final size:17
Alignment explanation
Indices: 347017--347058 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
347007 TATTGCCAAA
347017 GAAATGAAAAAAAA-AG
1 GAAATGAAAAAAAAGAG
347033 GAAATGAAAAAAAAGAG
1 GAAATGAAAAAAAAGAG
347050 GAAATGAAA
1 GAAATGAAA
347059 CGTGATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (17 bp):
GAAATGAAAAAAAAGAG
Found at i:347045 original size:17 final size:17
Alignment explanation
Indices: 347017--347058 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
347007 TATTGCCAAA
347017 GAAATG-AAAAAAAAAG
1 GAAATGAAAAAAAAAAG
*
347033 GAAATGAAAAAAAAGAG
1 GAAATGAAAAAAAAAAG
347050 GAAATGAAA
1 GAAATGAAA
347059 CGTGATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (17 bp):
GAAATGAAAAAAAAAAG
Found at i:347759 original size:21 final size:21
Alignment explanation
Indices: 347733--347775 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
347723 TCCCCCCTTT
347733 CCTCTTCCTATAAAAACCACA
1 CCTCTTCCTATAAAAACCACA
*
347754 CCTCTTCCTATCAAAACCACA
1 CCTCTTCCTATAAAAACCACA
347775 C
1 C
347776 TCAACACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTCTTCCTATAAAAACCACA
Found at i:349620 original size:21 final size:21
Alignment explanation
Indices: 349594--349648 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
349584 ATGTACATTT
* *
349594 TGCAACCGTTTCAGATGGTAC
1 TGCAACCATTTCAGATGGCAC
349615 TGCAACCATATT-AGATGGCAC
1 TGCAACCAT-TTCAGATGGCAC
349636 TGCAACCATTTCA
1 TGCAACCATTTCA
349649 TATACCACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCAACCATTTCAGATGGCAC
Found at i:351252 original size:182 final size:182
Alignment explanation
Indices: 350945--351303 Score: 673
Period size: 182 Copynumber: 2.0 Consensus size: 182
350935 TTTATTACTA
* *
350945 GTAAATGGTGTGCCCCATTTCAGGTCAAATTGATAGCCTCAGCCAAGTTGGTCGTCATGTGTCTA
1 GTAAATGGTGTACCCCATTTAAGGTCAAATTGATAGCCTCAGCCAAGTTGGTCGTCATGTGTCTA
*
351010 TATCGATATCCACCATCATATGTATTTGTCCACATTTCTTTTGTTGATGGGGCTGATGTAATTGT
66 TATCGATATCCACCATCATATGTATTTGTCAACATTTCTTTTGTTGATGGGGCTGATGTAATTGT
*
351075 ATCATTGCTCGTTCTTTCCTCGCAAATCTTGAAGCATGGACTCAAATTGCTG
131 ATCATTGCTCGTTCTTTCCTCGCAAATCTTGAAGCATGAACTCAAATTGCTG
351127 GTAAATGGTGTACCCCATTTAAGGTCAAATTGATAGCCTCAGCCAAGTTGGTCGTCATGTGTCTA
1 GTAAATGGTGTACCCCATTTAAGGTCAAATTGATAGCCTCAGCCAAGTTGGTCGTCATGTGTCTA
351192 TATCGATATCCACCATCATATGTATTTGTCAACATTTCTTTTGTTGATGGGGCTGATGTAATTGT
66 TATCGATATCCACCATCATATGTATTTGTCAACATTTCTTTTGTTGATGGGGCTGATGTAATTGT
*
351257 ATCATTTCTCGTTCTTTCCTCGCAAATCTTGAAGCATGAACTCAAAT
131 ATCATTGCTCGTTCTTTCCTCGCAAATCTTGAAGCATGAACTCAAAT
351304 ATTTCAGGCA
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
182 172 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (182 bp):
GTAAATGGTGTACCCCATTTAAGGTCAAATTGATAGCCTCAGCCAAGTTGGTCGTCATGTGTCTA
TATCGATATCCACCATCATATGTATTTGTCAACATTTCTTTTGTTGATGGGGCTGATGTAATTGT
ATCATTGCTCGTTCTTTCCTCGCAAATCTTGAAGCATGAACTCAAATTGCTG
Found at i:361994 original size:18 final size:18
Alignment explanation
Indices: 361968--362002 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
361958 TGTGACATTC
*
361968 TTGAGAGAACCATCTTAT
1 TTGAAAGAACCATCTTAT
*
361986 TTGAAAGAACTATCTTA
1 TTGAAAGAACCATCTTA
362003 ATCCATTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGAAAGAACCATCTTAT
Found at i:368428 original size:20 final size:20
Alignment explanation
Indices: 368403--368440 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
368393 TCTTTATTAT
* *
368403 AAAATAATTATTTGATTTAG
1 AAAATAATGAATTGATTTAG
368423 AAAATAATGAATTGATTT
1 AAAATAATGAATTGATTT
368441 TTCTCATTAA
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:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAATAATGAATTGATTTAG
Found at i:376567 original size:3 final size:3
Alignment explanation
Indices: 376559--376586 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
376549 TCGAGTAAAG
376559 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
376587 AACCCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:376802 original size:14 final size:14
Alignment explanation
Indices: 376779--376819 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
376769 TAATGGAAAG
*
376779 TAATCCCTGC-TAA
1 TAATCTCTGCATAA
376792 TAAATCTCTGCATAA
1 T-AATCTCTGCATAA
376807 TAATCTCTGCATA
1 TAATCTCTGCATA
376820 TAGATAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 1 0.04
14 20 0.80
15 4 0.16
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (14 bp):
TAATCTCTGCATAA
Found at i:378662 original size:61 final size:60
Alignment explanation
Indices: 378586--378706 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 60
378576 TTAAAAAAAT
* *
378586 TCAAAACGATATCGTTTTATTAGAA-TCTTTTAATGAAAAAAATGATTTTAATGAGATTCAA
1 TCAAAACGACATCGTTTTATTA-AAGTCTTTTAAT-AAAAAAATAATTTTAATGAGATTCAA
* *
378647 TCAAAACGACGTCGTTTTATTAAAGTCTTTTAATAAAAAAATAATTTTAATTAGATTCAA
1 TCAAAACGACATCGTTTTATTAAAGTCTTTTAATAAAAAAATAATTTTAATGAGATTCAA
378707 ACCAAAACCC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
60 26 0.47
61 29 0.53
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (60 bp):
TCAAAACGACATCGTTTTATTAAAGTCTTTTAATAAAAAAATAATTTTAATGAGATTCAA
Found at i:382079 original size:18 final size:16
Alignment explanation
Indices: 382037--382083 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
382027 TTCATATTAA
382037 AAAAGATAAAAAAGAT
1 AAAAGATAAAAAAGAT
**
382053 AAACCATAAGAAAGAGAT
1 AAAAGATAA-AAA-AGAT
382071 AAAAGATAAAAAA
1 AAAAGATAAAAAA
382084 AAGATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 11 0.44
ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAAGATAAAAAAGAT
Found at i:382088 original size:18 final size:18
Alignment explanation
Indices: 382044--382092 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
382034 TAAAAAAGAT
*
382044 AAAAAAGATAAACCATAA
1 AAAAAAGATAAAACATAA
* * *
382062 GAAAGAGATAAAAGATAA
1 AAAAAAGATAAAACATAA
382080 AAAAAAGATAAAA
1 AAAAAAGATAAAA
382093 AAAAATAACG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.73, C:0.04, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAAGATAAAACATAA
Found at i:382095 original size:12 final size:11
Alignment explanation
Indices: 382071--382100 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
382061 AGAAAGAGAT
382071 AAAAGATAAAA
1 AAAAGATAAAA
382082 AAAAGATAAAA
1 AAAAGATAAAA
382093 AAAA-ATAA
1 AAAAGATAA
382101 CGACCGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAGATAAAA
Found at i:383615 original size:37 final size:37
Alignment explanation
Indices: 383539--383615 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
383529 TTTTTATATT
*
383539 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
383576 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
383613 TTT
1 TTT
383616 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:384507 original size:2 final size:2
Alignment explanation
Indices: 384500--384547 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
384490 TAAATTTAAT
384500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
384542 TA TA TA
1 TA TA TA
384548 AACTCAAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:388437 original size:20 final size:20
Alignment explanation
Indices: 388412--388451 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
388402 AGCAACAGAA
*
388412 TAAAAATGATTCTATCTAAT
1 TAAAAATGATACTATCTAAT
388432 TAAAAATGATACTATCTAAT
1 TAAAAATGATACTATCTAAT
388452 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATACTATCTAAT
Found at i:388541 original size:20 final size:20
Alignment explanation
Indices: 388516--388554 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
388506 TAATAGAATA
*
388516 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
388536 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
388555 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:388545 original size:50 final size:51
Alignment explanation
Indices: 388408--388552 Score: 240
Period size: 50 Copynumber: 2.8 Consensus size: 51
388398 AATTAGCAAC
*
388408 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATACTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCT-ATAACTAAT
388459 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCT-TAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTATAACTAAT
*
388510 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTA
388553 ATATTTAATT
Statistics
Matches: 89, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
50 36 0.40
51 18 0.20
52 5 0.06
53 30 0.34
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (51 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTATAACTAAT
Found at i:393138 original size:20 final size:20
Alignment explanation
Indices: 393113--393152 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
393103 AGCAACAGAA
393113 TAAAAATGAT-TCTATCTAAT
1 TAAAAATGATCT-TATCTAAT
393133 TAAAAATGATCTTATCTAAT
1 TAAAAATGATCTTATCTAAT
393153 AACTAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATGATCTTATCTAAT
Found at i:393195 original size:20 final size:21
Alignment explanation
Indices: 393166--393205 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
393156 TAATAGAATA
*
393166 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
393187 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
393206 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:393244 original size:20 final size:20
Alignment explanation
Indices: 393219--393257 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
393209 TAATAGAATA
*
393219 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
393239 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
393258 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:393248 original size:52 final size:52
Alignment explanation
Indices: 393109--393258 Score: 266
Period size: 52 Copynumber: 2.9 Consensus size: 52
393099 AATTAGCAAC
*
393109 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCTTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
393160 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
393213 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
393259 TTTAATTTAG
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 5 0.05
52 45 0.47
53 45 0.47
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:417280 original size:14 final size:14
Alignment explanation
Indices: 417260--417302 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
417250 GTCATCTGTT
417260 CGAACATAAATGAA
1 CGAACATAAATGAA
*
417274 TGAACATAAATGAA
1 CGAACATAAATGAA
*
417288 CGAACATAAACGAA
1 CGAACATAAATGAA
417302 C
1 C
417303 ATATAATCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.56, C:0.16, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:420386 original size:17 final size:18
Alignment explanation
Indices: 420360--420399 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
420350 ATTATATAGA
420360 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
420376 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
420394 TATTAT
1 TATTAT
420400 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:420410 original size:2 final size:2
Alignment explanation
Indices: 420403--420429 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
420393 TTATTATACG
420403 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
420430 TTTAAATTAT
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:420667 original size:2 final size:2
Alignment explanation
Indices: 420662--420700 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
420652 CTTATAACTT
420662 TA TA TA 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 TA TA TA T
420701 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:421078 original size:14 final size:14
Alignment explanation
Indices: 421059--421106 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
421049 CCTTATCTTA
*
421059 TTTATTTATTTTAT
1 TTTATTCATTTTAT
*
421073 TTTATTCCTTTTAT
1 TTTATTCATTTTAT
421087 TTTATTC-TCTTTAT
1 TTTATTCAT-TTTAT
*
421101 CTTATT
1 TTTATT
421107 TGTTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 1 0.03
14 29 0.97
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTCATTTTAT
Done.