Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007910.1 Hibiscus syriacus cultivar Beakdansim tig00110306_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: 704475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:249479 original size:9 final size:9
Alignment explanation
Indices: 249465--249494 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
249455 GCATTGATTT
249465 ACCGGTTTG
1 ACCGGTTTG
*
249474 ACCGGTCTG
1 ACCGGTTTG
249483 ACCGGTTTG
1 ACCGGTTTG
249492 ACC
1 ACC
249495 CGACCCAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.13, C:0.30, G:0.30, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:249586 original size:29 final size:29
Alignment explanation
Indices: 249516--249684 Score: 184
Period size: 28 Copynumber: 5.9 Consensus size: 29
249506 GACCGGATGT
* * ** *
249516 TATTTTCATAAATATATTTAAAAATGTGC
1 TATTTTCGTAAATATTTTTAAAAGGGTGA
*
249545 T-TTTTTGTAAATATTTTTAAAAGGGTGA
1 TATTTTCGTAAATATTTTTAAAAGGGTGA
**
249573 TATTTTCGTAAATATTTTTTAAAAAAGTGA
1 TATTTTCGTAAATA-TTTTTAAAAGGGTGA
* *
249603 TATTTTCATAAATATTTTTAAACGGGT-A
1 TATTTTCGTAAATATTTTTAAAAGGGTGA
* *
249631 CTA-TTTCGTAAATATTTTTAAAAGGTTGT
1 -TATTTTCGTAAATATTTTTAAAAGGGTGA
249660 TATTTT-GTAAATATTTTTAAAAGGG
1 TATTTTCGTAAATATTTTTAAAAGGG
249685 AGTTAATTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
28 64 0.55
29 27 0.23
30 26 0.22
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.47
Consensus pattern (29 bp):
TATTTTCGTAAATATTTTTAAAAGGGTGA
Found at i:249664 original size:87 final size:85
Alignment explanation
Indices: 249516--249681 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 85
249506 GACCGGATGT
* * * *
249516 TATTTTCATAAATATATTTAAAAATGTGCTTTTTTGTAAATATTTTTAAAAGGGTGATATTTTCG
1 TATTTTCATAAATATATTTAAAAAGGTACTATTTCGTAAATATTTTTAAAAGGGTGATATTTT-G
249581 TAAATATTTTTTAAAAAAGTGA
65 TAAATA-TTTTTAAAAAAGTGA
* ** * *
249603 TATTTTCATAAATATTTTTAAACGGGTACTATTTCGTAAATATTTTTAAAAGGTTGTTATTTTGT
1 TATTTTCATAAATATATTTAAAAAGGTACTATTTCGTAAATATTTTTAAAAGGGTGATATTTTGT
249668 AAATATTTTTAAAA
66 AAATATTTTTAAAA
249682 GGGAGTTAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
85 9 0.13
86 7 0.10
87 54 0.77
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (85 bp):
TATTTTCATAAATATATTTAAAAAGGTACTATTTCGTAAATATTTTTAAAAGGGTGATATTTTGT
AAATATTTTTAAAAAAGTGA
Found at i:256887 original size:18 final size:18
Alignment explanation
Indices: 256842--256887 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
256832 GAACCGGTTT
*
256842 GACCCGACCAGTTGACCC
1 GACCCGACCCGTTGACCC
*
256860 AACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
256878 GACCCGACCC
1 GACCCGACCC
256888 AGGTGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.50, G:0.20, T:0.09
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:256954 original size:29 final size:29
Alignment explanation
Indices: 256888--257105 Score: 255
Period size: 29 Copynumber: 7.6 Consensus size: 29
256878 GACCCGACCC
256888 AGGTGTTATTTTCGTAAATATTTTTAAAA
1 AGGTGTTATTTTCGTAAATATTTTTAAAA
*
256917 A-GTGTTATTTTCGTATATATTTTTAAAA
1 AGGTGTTATTTTCGTAAATATTTTTAAAA
*
256945 AGGTGATATTTTCGTAAATATTTTTAAAA
1 AGGTGTTATTTTCGTAAATATTTTTAAAA
* * *
256974 A-ATGATATTTT-GTAAATATTTTTAAAT
1 AGGTGTTATTTTCGTAAATATTTTTAAAA
* * *
257001 GGGTGCTAGTTTCGTAAATATTTTTAAAA
1 AGGTGTTATTTTCGTAAATATTTTTAAAA
* * *
257030 GGGTGCTATTTTTGTAAATATTTTTAAAAA
1 AGGTGTTATTTTCGTAAATATTTTT-AAAA
* **
257060 ATGTGTTATTTTTATAAATATTTTTAAAA
1 AGGTGTTATTTTCGTAAATATTTTTAAAA
*
257089 GGGTGTTAGTTTT-GTAA
1 AGGTGTTA-TTTTCGTAA
257106 TTAATTTATG
Statistics
Matches: 165, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
27 15 0.09
28 43 0.26
29 78 0.47
30 29 0.18
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.49
Consensus pattern (29 bp):
AGGTGTTATTTTCGTAAATATTTTTAAAA
Found at i:257040 original size:85 final size:85
Alignment explanation
Indices: 256894--257105 Score: 273
Period size: 85 Copynumber: 2.4 Consensus size: 85
256884 ACCCAGGTGT
** * *
256894 TATTTTCGTAAATATTTTTAAAAAGTGTTATTTTCGTATATATTTTTAAAAAGGTGATATTTTCG
1 TATTTT-GTAAATATTTTTAAAGGGTGTTAGTTTCGTAAATATTTTTAAAAAGGTGATATTTTCG
256959 TAAATATTTTTAAAAAA-TGA
65 TAAATATTTTTAAAAAAGTGA
* * * *
256979 TATTTTGTAAATATTTTTAAATGGGTGCTAGTTTCGTAAATATTTTTAAAAGGGTGCTATTTTTG
1 TATTTTGTAAATATTTTTAAA-GGGTGTTAGTTTCGTAAATATTTTTAAAAAGGTGATATTTTCG
*
257044 TAAATATTTTTAAAAAATGTGT
65 TAAATATTTTTAAAAAA-GTGA
* *
257066 TATTTTTATAAATATTTTTAAAAGGGTGTTAGTTTTGTAA
1 TA-TTTTGTAAATATTTTT-AAAGGGTGTTAGTTTCGTAA
257106 TTAATTTATG
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
84 15 0.14
85 58 0.53
87 4 0.04
88 30 0.27
89 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (85 bp):
TATTTTGTAAATATTTTTAAAGGGTGTTAGTTTCGTAAATATTTTTAAAAAGGTGATATTTTCGT
AAATATTTTTAAAAAAGTGA
Found at i:257131 original size:59 final size:59
Alignment explanation
Indices: 256902--257113 Score: 159
Period size: 59 Copynumber: 3.7 Consensus size: 59
256892 GTTATTTTCG
* * * * * * **
256902 TAAATATTTTTAAAA-AGTGTTA-TTTTCGTATATAT-TTTTAAAAAGGTGATATTTTCG
1 TAAATATTTTTAAAAGGGTGCTAGTTTT-GTAAATATATTTAAAAAATGTGCTATTTTTA
** * * *** * **
256959 TAAATATTTTTAAAA-AATGATA-TTTTGTAAATAT-TTTTAAATGGGTGCTAGTTTCG
1 TAAATATTTTTAAAAGGGTGCTAGTTTTGTAAATATATTTAAAAAATGTGCTATTTTTA
* * *
257015 TAAATATTTTTAAAAGGGTGCTATTTTTGTAAATATTTTTAAAAAATGTGTTATTTTTA
1 TAAATATTTTTAAAAGGGTGCTAGTTTTGTAAATATATTTAAAAAATGTGCTATTTTTA
* *
257074 TAAATATTTTTAAAAGGGTGTTAGTTTTGTAATTA-ATTTA
1 TAAATATTTTTAAAAGGGTGCTAGTTTTGTAAATATATTTA
257114 TGTTATGGTG
Statistics
Matches: 130, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
56 40 0.31
57 28 0.22
58 16 0.12
59 46 0.35
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.49
Consensus pattern (59 bp):
TAAATATTTTTAAAAGGGTGCTAGTTTTGTAAATATATTTAAAAAATGTGCTATTTTTA
Found at i:270538 original size:16 final size:16
Alignment explanation
Indices: 270511--270544 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
270501 CCCAAGCCTT
270511 TTCTTGTTTGTTATCCC
1 TTCTTGTTTGTTA-CCC
270528 TTCTT-TTTGTTACCC
1 TTCTTGTTTGTTACCC
270543 TT
1 TT
270545 TTCAGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.06, C:0.24, G:0.09, T:0.62
Consensus pattern (16 bp):
TTCTTGTTTGTTACCC
Found at i:272017 original size:82 final size:81
Alignment explanation
Indices: 271901--272075 Score: 219
Period size: 82 Copynumber: 2.2 Consensus size: 81
271891 CTAAGTCTCG
* * ** *
271901 TGATTTGTGTTTGCTATGGTTTGTTTTCTGAACTTCGTATCACACATGATAGTCTAT-GGGGAAA
1 TGATTTGTGTTTTCTACGGTTTGTTTTCCAAACTTCGCATCACACATGATAGTCT-TCGGGGAAA
* * *
271965 TAAATGTATGAAATTAAT
65 TAAAGGT-CGAAAATAAT
* **
271983 TGATTTGTGTTTTTTACGGTTTGTTTTCCAAACTTCGCATGGCACATGATAGTCTTCGGGGAAAT
1 TGATTTGTGTTTTCTACGGTTTGTTTTCCAAACTTCGCATCACACATGATAGTCTTCGGGGAAAT
272048 AAAGGTCGAAAATAAT
66 AAAGGTCGAAAATAAT
272064 TGATTT-TGTTTT
1 TGATTTGTGTTTT
272076 GCTATTTCTA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
80 6 0.07
81 15 0.19
82 60 0.74
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (81 bp):
TGATTTGTGTTTTCTACGGTTTGTTTTCCAAACTTCGCATCACACATGATAGTCTTCGGGGAAAT
AAAGGTCGAAAATAAT
Found at i:273133 original size:57 final size:56
Alignment explanation
Indices: 272973--273220 Score: 189
Period size: 57 Copynumber: 4.3 Consensus size: 56
272963 TAAATTGTTG
* * * * *
272973 TTTCTTGAGAATCTTAAATGATTATATTTTGTAAAATAAAAAATAAATCATTGAATTTAT
1 TTTC-TGA-AATCTTGAATGATTCTATTTTGT-AAA-AAGAAATAAATCGTTAAATTTAT
* * * *
273033 TTTCCGTTG-AATATT-ACATGATTCTAGTTTGTAAAAGGAAATAAATCGTCAAATTTAT
1 TTT-C--TGAAATCTTGA-ATGATTCTATTTTGTAAAAAGAAATAAATCGTTAAATTTAT
* * * * *
273091 TTTCTCGAAATCTTGAATGATTCCATTTTGTAGAACGAAATAAATTGTTGAATTTAT
1 TTTCT-GAAATCTTGAATGATTCTATTTTGTAAAAAGAAATAAATCGTTAAATTTAT
* * * *
273148 TTT-TGTAGAATGTTGGATGATTATGTTTTGTAAAAAGAAATAAATCGTTAAATTTA-
1 TTTCTG-A-AATCTTGAATGATTCTATTTTGTAAAAAGAAATAAATCGTTAAATTTAT
273204 TTTCTTGGAAATCTTGA
1 TTTC-T-GAAATCTTGA
273221 TATGTTTGTA
Statistics
Matches: 150, Mismatches: 27, Indels: 25
0.74 0.13 0.12
Matches are distributed among these distances:
55 2 0.01
56 6 0.04
57 88 0.59
58 24 0.16
59 5 0.03
60 21 0.14
61 1 0.01
62 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (56 bp):
TTTCTGAAATCTTGAATGATTCTATTTTGTAAAAAGAAATAAATCGTTAAATTTAT
Found at i:276667 original size:19 final size:19
Alignment explanation
Indices: 276645--276686 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
276635 TTATGAACTT
276645 TGATATCTG-TTATGATATC
1 TGATATCTGATT-TGATATC
* *
276664 TGATTTCTGATTTGATTTC
1 TGATATCTGATTTGATATC
276683 TGAT
1 TGAT
276687 CTCTATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (19 bp):
TGATATCTGATTTGATATC
Found at i:286995 original size:26 final size:27
Alignment explanation
Indices: 286945--286995 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
286935 TAGTGTTTGG
286945 GGGTATTTTGGTCATTTTAGAGTTTAT
1 GGGTATTTTGGTCATTTTAGAGTTTAT
286972 GGGTATTTTGGTC-TTTTAGAGTTT
1 GGGTATTTTGGTCATTTTAGAGTTT
286996 GAAGGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.16, C:0.04, G:0.27, T:0.53
Consensus pattern (27 bp):
GGGTATTTTGGTCATTTTAGAGTTTAT
Found at i:287002 original size:26 final size:27
Alignment explanation
Indices: 286946--287005 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
286936 AGTGTTTGGG
*
286946 GGTATTTTGGTCATTTTAGAGTTTATG
1 GGTATTTTGGTCATTTTAGAGTTTATA
286973 GGTATTTTGGTC-TTTTAGAGTTTGA-A
1 GGTATTTTGGTCATTTTAGAGTTT-ATA
286999 GGTATTT
1 GGTATTT
287006 CGATTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.18, C:0.03, G:0.27, T:0.52
Consensus pattern (27 bp):
GGTATTTTGGTCATTTTAGAGTTTATA
Found at i:290386 original size:21 final size:22
Alignment explanation
Indices: 290361--290401 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
290351 CATAAATGAA
*
290361 AATAATTATGGGA-TTAAATTG
1 AATAATAATGGGAGTTAAATTG
*
290382 AATAATAATTGGAGTTAAAT
1 AATAATAATGGGAGTTAAAT
290402 GCCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (22 bp):
AATAATAATGGGAGTTAAATTG
Found at i:296070 original size:56 final size:57
Alignment explanation
Indices: 296001--296110 Score: 195
Period size: 56 Copynumber: 1.9 Consensus size: 57
295991 GGAGAACATG
*
296001 GTCTTAGTACTCTGAATACAATCATGAAGAACCAAGAATC-TTGGTTGATCAGAGTA
1 GTCTGAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGAGTA
*
296057 GTCTGAGTACTCTGAATATAATCATGAAGAACCAAGAATCTTTGGTTGATCAGA
1 GTCTGAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGA
296111 TCATTGCCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 38 0.75
57 13 0.25
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (57 bp):
GTCTGAGTACTCTGAATACAATCATGAAGAACCAAGAATCTTTGGTTGATCAGAGTA
Found at i:298352 original size:16 final size:16
Alignment explanation
Indices: 298331--298362 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
298321 ATTTCAGAGG
298331 ACCGAAATAAAAGGTC
1 ACCGAAATAAAAGGTC
298347 ACCGAAATAAAAGGTC
1 ACCGAAATAAAAGGTC
298363 TAGTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
ACCGAAATAAAAGGTC
Found at i:299589 original size:84 final size:83
Alignment explanation
Indices: 299277--299831 Score: 532
Period size: 84 Copynumber: 6.7 Consensus size: 83
299267 TTTAAGACAA
* * * * *
299277 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCAACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
299342 CTCAGCTCCAAGGCGCAT
66 CTCAGCTCCAAGGCACAT
* * * * * * * * *
299360 AATTTGTAGCATAGCTTAAGTCAAGAAAGGCTATCTG---CCAAAG-CCCTCAAGTTCGACTATG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
299421 CTCAGCTACGAGGGCACAT
66 CTCAGCT-CCAAGGCACAT
* * * * * * * * *
299440 CATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTCACCAAACACCTTCGCGTTTGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
299505 CTCAGCTCCAAGGCATAT
66 CTCAGCTCCAAGGCACAT
*
299523 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
*
299588 GCTCAGCTCCAAGGCGCAT
65 GCTCAGCTCCAAGGCACAT
* * * * *
299607 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT---TCCAAAGACCTTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
** *
299669 CTCAGCTTTGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * * * *
299688 TATTTACAACATAACTCAAGGCTAGAA-GGTTATCTGTCACCAAAAGACCTTAGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTAC
299752 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* *** * * *
299771 CATTTGCAGTAGGGCTTAAGTCGAGAAGGGTTATCTTCCAACCGAAGACCTTCAAGTTCGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
299832 TTACACTCGG
Statistics
Matches: 370, Mismatches: 89, Indels: 25
0.76 0.18 0.05
Matches are distributed among these distances:
79 21 0.06
80 76 0.21
81 28 0.08
83 102 0.28
84 140 0.38
85 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:299777 original size:248 final size:247
Alignment explanation
Indices: 299277--299831 Score: 799
Period size: 248 Copynumber: 2.2 Consensus size: 247
299267 TTTAAGACAA
* * * *
299277 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCAACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
299341 GCTCAGCTCCAAGGCGCATAATTTGTAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAGCCC
66 GCTCAGCTCCAAGGCGCATAATTTGCAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAGCCC
** * *
299406 TCAAGTTCGACTATGCTCAGCTACGAGGGCACATCATTTACAGCATAACTCAAGGCTATAAGGGT
131 TCAAGTTCGACTACACTCAGCTACGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
* * *
299471 TATCTGTCACCAAACACCTTCGCGTTTGACTACGCTCAGCTCCAAGGCATAT
196 TATCTGTCACCAAACACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
*
299523 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
299588 GCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTCCAAAGACC
66 GCTCAGCTCCAAGGCGCATAATTTGCAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAG-CC
* * * ** *
299653 TTCGAGTTCGATTACACTCAGCTTTGAGGGCACATTATTTACAACATAACTCAAGGCTAGAA-GG
130 CTCAAGTTCGACTACACTCAGCTACGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGG
*
299717 TTATCTGTCACCAAAAGACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
195 TTATCTGTCACC-AAACACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
* *** * * *
299771 CATTTGCAGTAGGGCTTAAGTCGAGAAGGGTTATCTTCCAACCGAAGACCTTCAAGTTCGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
299832 TTACACTCGG
Statistics
Matches: 274, Mismatches: 32, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
246 37 0.14
247 93 0.34
248 144 0.53
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (247 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCGCATAATTTGCAGCATAGCTTAAGTCAAGAAAGGCTATCTGCCAAAGCCC
TCAAGTTCGACTACACTCAGCTACGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGT
TATCTGTCACCAAACACCTTAGAGTTTGACTACGCTCAGCTCCAAGGCACAT
Found at i:300539 original size:39 final size:36
Alignment explanation
Indices: 300484--300671 Score: 122
Period size: 37 Copynumber: 5.1 Consensus size: 36
300474 TTTTTTAAAA
300484 AAAAAAGCATTTTTGAAAACATATAATTATATAGTTTTCT
1 AAAAAA-CA-TTTTGAAAA-ATATAATTATATAGTTTT-T
*
300524 AAAAAAACATTTTG--AAATAT-ATAATATAG-TTTT
1 -AAAAAACATTTTGAAAAATATAATTATATAGTTTTT
** * *
300557 CGAAAACATTTT-AAAAATGTATATAATATATGGTTTTT
1 AAAAAACATTTTGAAAAA--TATA-ATTATATAGTTTTT
* *
300595 AAAAAACAGTTTGAAAAATATTTATAATATATAGTTTTT
1 AAAAAACATTTTGAAAAATA--TA-ATTATATAGTTTTT
* * *
300634 --AAAACATTTTGAAAACTATATAGTATAT-GATTTT
1 AAAAAACATTTTGAAAAATATA-ATTATATAGTTTTT
300668 AAAA
1 AAAA
300672 CATTTTTTAG
Statistics
Matches: 121, Mismatches: 14, Indels: 29
0.74 0.09 0.18
Matches are distributed among these distances:
32 10 0.08
33 4 0.03
34 8 0.07
35 20 0.17
36 6 0.05
37 26 0.21
38 13 0.11
39 26 0.21
40 2 0.02
41 6 0.05
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (36 bp):
AAAAAACATTTTGAAAAATATAATTATATAGTTTTT
Found at i:300580 original size:35 final size:36
Alignment explanation
Indices: 300541--300782 Score: 135
Period size: 35 Copynumber: 6.6 Consensus size: 36
300531 CATTTTGAAA
300541 TATATAATATA-G-TTTTCGAAAACA-TTTTAAAAATG
1 TATATAATATATGATTTT--AAAACATTTTTAAAAATG
* * * *
300576 TATATAATATATGGTTTTTAAAAAACAGTTTGAAAAATA
1 TATATAATATAT-GATTTT--AAAACATTTTTAAAAATG
* * * *
300615 TTTATAATATATAGTTTTTAAAACA-TTTTGAAAA-C
1 TATATAATATAT-GATTTTAAAACATTTTTAAAAATG
*
300650 TATATAGTATATGATTTTAAAACATTTTTTAGAAAGTATG
1 TATATAATATATGATTTTAAAACA-TTTTTA-AAA--ATG
* * *
300690 TATATAATATATAATTTTAAAATATTATTTGAAAA--
1 TATATAATATATGATTTTAAAACATT-TTTAAAAATG
* ** *
300725 TATAT-ATCATATGACTTT--AATTTTTTTAAAACATA
1 TATATAAT-ATATGATTTTAAAACATTTTTAAAA-ATG
*
300760 TATATAATATATTATTTTTAAAA
1 TATATAATATATGA-TTTTAAAA
300783 TGTTCTTTTT
Statistics
Matches: 164, Mismatches: 24, Indels: 35
0.74 0.11 0.16
Matches are distributed among these distances:
32 6 0.04
33 6 0.04
34 13 0.08
35 44 0.27
36 16 0.10
37 11 0.07
38 12 0.07
39 32 0.20
40 24 0.15
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
TATATAATATATGATTTTAAAACATTTTTAAAAATG
Found at i:300593 original size:37 final size:36
Alignment explanation
Indices: 300541--300736 Score: 123
Period size: 39 Copynumber: 5.3 Consensus size: 36
300531 CATTTTGAAA
300541 TATATAATATA--GTTTTCGAAAACA-TTTTAAAAATG
1 TATATAATATATGGTTTT--AAAACATTTTTAAAAATG
* * *
300576 TATATAATATATGGTTTTTAAAAAACAGTTTGAAAAATA
1 TATATAATATATGG-TTTT--AAAACATTTTTAAAAATG
* * * *
300615 TTTATAATATATAGTTTTTAAAACA-TTTTGAAAA-C
1 TATATAATATAT-GGTTTTAAAACATTTTTAAAAATG
* *
300650 TATATAGTATATGATTTTAAAACATTTTTTAGAAAGTATG
1 TATATAATATATGGTTTTAAAACA-TTTTTA-AAA--ATG
** * * *
300690 TATATAATATATAATTTTAAAATATTATTTGAAAATA
1 TATATAATATATGGTTTTAAAACATT-TTTAAAAATG
*
300727 TATATCATAT
1 TATATAATAT
300737 GACTTTAATT
Statistics
Matches: 129, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
34 11 0.09
35 21 0.16
36 11 0.09
37 21 0.16
38 10 0.08
39 30 0.23
40 25 0.19
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TATATAATATATGGTTTTAAAACATTTTTAAAAATG
Found at i:301888 original size:26 final size:26
Alignment explanation
Indices: 301854--301920 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
301844 ATGTATTGCA
301854 AAACGACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
*
301880 AAACAACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
301906 AAACGACGTAGTTTT
1 AAACGACGTAGTTTT
301921 ATCCCATAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTGCAAG
Found at i:302085 original size:4 final size:4
Alignment explanation
Indices: 302076--302117 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
302066 CACTTTCTGC
* * *
302076 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
302118 TTGTTTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:302236 original size:23 final size:21
Alignment explanation
Indices: 302185--302242 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 21
302175 ATATCTAACC
*
302185 TTTTTAGTTTTTTATTTCATT
1 TTTTTATTTTTTTATTTCATT
302206 TGGATTTTATTTTTTTATTTCCATT
1 T---TTTTATTTTTTTATTT-CATT
302231 ATTTTTATTTTT
1 -TTTTTATTTTT
302243 ATTTTTACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 1 0.03
23 10 0.32
24 15 0.48
25 4 0.13
26 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTATTTTTTTATTTCATT
Found at i:302420 original size:10 final size:11
Alignment explanation
Indices: 302400--302459 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 11
302390 TTTGACTTTG
302400 TTTTATTATTA
1 TTTTATTATTA
302411 TTTT-TTATTA
1 TTTTATTATTA
* * *
302421 TGTTAGTATTT
1 TTTTATTATTA
302432 TATTTAGTTAATTA
1 T-TTTA-TT-ATTA
302446 TTATTATTATTA
1 TT-TTATTATTA
302458 TT
1 TT
302460 ATTTTGATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
10 9 0.24
11 9 0.24
12 9 0.24
13 4 0.11
14 7 0.18
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:302915 original size:35 final size:35
Alignment explanation
Indices: 302844--302989 Score: 114
Period size: 35 Copynumber: 4.0 Consensus size: 35
302834 TATAGGTTTT
* *
302844 TTTAAAAAAGCATTTTTGAAAACATATATATTATATAG
1 TTTAAAAAAACA-TTTT-AAAA-ATATATATAATATAG
*
302882 TTTAAAAAAAACATTTT-GAAATATATATAATATAG
1 TTT-AAAAAAACATTTTAAAAATATATATAATATAG
*** *
302917 TTTTCGAAAACATTTTAAAAATGTATATAATATATGG
1 TTTAAAAAAACATTTTAAAAATATATATAATATA--G
** * *
302954 TTTTTTAAAAACAGTTTGAAAAATATTTATAATATA
1 -TTTAAAAAAACA-TTTTAAAAATATATATAATATA
302990 CAGTTTTTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
34 10 0.11
35 32 0.36
36 2 0.02
37 1 0.01
38 17 0.19
39 27 0.30
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (35 bp):
TTTAAAAAAACATTTTAAAAATATATATAATATAG
Found at i:302957 original size:37 final size:36
Alignment explanation
Indices: 302889--303037 Score: 126
Period size: 35 Copynumber: 4.1 Consensus size: 36
302879 TAGTTTAAAA
*
302889 AAAACATTTT-GAAATATATATAATATA--GTTTTCG
1 AAAACATTTTAAAAATATATATAATATATGGTTTT-G
* *
302923 AAAACATTTTAAAAATGTATATAATATATGGTTTTTTA
1 AAAACATTTTAAAAATATATATAATATATGG--TTTTG
* * ** *
302961 AAAACAGTTTGAAAAATATTTATAATATACAGTTTTT
1 AAAACA-TTTTAAAAATATATATAATATATGGTTTTG
* * * *
302998 AAAACATTTTGAAAA-CTATATAGTATATGATTTTG
1 AAAACATTTTAAAAATATATATAATATATGGTTTTG
303033 AAAAC
1 AAAAC
303038 TATATAGTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
34 10 0.11
35 33 0.36
36 7 0.08
37 11 0.12
38 6 0.07
39 24 0.26
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (36 bp):
AAAACATTTTAAAAATATATATAATATATGGTTTTG
Found at i:302976 original size:39 final size:36
Alignment explanation
Indices: 302900--303019 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 36
302890 AAACATTTTG
* *
302900 AAATATATATAATAT--AGTTTTCGAAAACATTTTAA
1 AAATATATATAATATACAGTTTT-TAAAACATTTGAA
* **
302935 AAATGTATATAATATATGGTTTTTTAAAAACAGTTTGAA
1 AAATATATATAATATACAG-TTTTT-AAAACA-TTTGAA
*
302974 AAATATTTATAATATACAGTTTTTAAAACATTTTGAA
1 AAATATATATAATATACAGTTTTTAAAACA-TTTGAA
*
303011 AACTATATA
1 AAATATATA
303020 GTATATGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
35 14 0.20
37 20 0.29
38 15 0.22
39 20 0.29
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (36 bp):
AAATATATATAATATACAGTTTTTAAAACATTTGAA
Found at i:302989 original size:74 final size:71
Alignment explanation
Indices: 302888--303031 Score: 173
Period size: 74 Copynumber: 2.0 Consensus size: 71
302878 ATAGTTTAAA
* *
302888 AAAAACATTTTGAAATATATATAATAT-AGTTTTCGAAAACATTTTAAAAATGTATATAATATAT
1 AAAAACAGTTTGAAATATATATAATATAAGTTTT-GAAAACATTTTAAAAA-CTATATAATATAT
*
302952 GGTTTTTT
64 GATTTTTT
* * * *
302960 AAAAACAGTTTGAAAAATATTTATAATATACAGTTTTTAAAACATTTTGAAAACTATATAGTATA
1 AAAAACAGTTTG--AAATATATATAATATA-AGTTTTGAAAACATTTTAAAAACTATATAATATA
303025 TGATTTT
63 TGATTTT
303032 GAAAACTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
72 11 0.18
74 30 0.49
75 14 0.23
76 6 0.10
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (71 bp):
AAAAACAGTTTGAAATATATATAATATAAGTTTTGAAAACATTTTAAAAACTATATAATATATGA
TTTTTT
Found at i:303030 original size:24 final size:24
Alignment explanation
Indices: 303003--303061 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
302993 TTTTTAAAAC
303003 ATTTTGAAAACTATATAGTATATG
1 ATTTTGAAAACTATATAGTATATG
303027 ATTTTGAAAACTATATAGTATATG
1 ATTTTGAAAACTATATAGTATATG
303051 ATTTTGAAAAC
1 ATTTTGAAAAC
303062 ATTTTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (24 bp):
ATTTTGAAAACTATATAGTATATG
Found at i:304279 original size:26 final size:26
Alignment explanation
Indices: 304218--304284 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
304208 ATGTATTGCA
304218 AAACGACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
** * *
304244 AAAAAACGTAATTTTGCCACTGCAGG
1 AAACGACGTAGTTTTGCCACTGCAAG
*
304270 AAACGGCGTAGTTTT
1 AAACGACGTAGTTTT
304285 ATCCCATAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTGCAAG
Found at i:304450 original size:4 final size:4
Alignment explanation
Indices: 304441--304480 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
304431 CACTTTCTGC
* *
304441 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
304481 ATATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:305316 original size:39 final size:37
Alignment explanation
Indices: 305219--305502 Score: 170
Period size: 35 Copynumber: 7.4 Consensus size: 37
305209 TGCTAATGGT
* *
305219 TTTTGAAATAGATATATATTATATAGGTTTTCTTTAAAAAGCA
1 TTTTGAAA-ATATATATATTATATA-G---T-TTTAAAAAACA
*
305262 TTTTTGAAAACATATATATTATATAGTTTTAAAAAAGCA
1 -TTTTGAAAATATATATATTATATAGTTTTAAAAAA-CA
**
305301 TTTTG-AAATATATATA--ATATAGTTTTCGAAAACA
1 TTTTGAAAATATATATATTATATAGTTTTAAAAAACA
* * * *
305335 TTTTAAAAATGTATATAATATATGGTTTTTAAAAAACA
1 TTTTGAAAATATATATATTATATAG-TTTTAAAAAACA
* * * *
305373 GTTTGAAAAATATTTATAATATATAGTTTT-TAAAACA
1 TTTTG-AAAATATATATATTATATAGTTTTAAAAAACA
* * *
305410 TTTTGAAAA-CTATATAGTATAT-GATTTT-GAAAACA
1 TTTTGAAAATATATATATTATATAG-TTTTAAAAAACA
* * * *
305445 TTTCTTAGAAAGTATGTATATAATATATAATTTTAAAATAC-
1 -TT-TT-GAAA--ATATATATATTATATAGTTTTAAAAAACA
*
305486 TATTTCAAAATATATAT
1 T-TTTGAAAATATATAT
305503 TATAAGATTT
Statistics
Matches: 196, Mismatches: 28, Indels: 39
0.75 0.11 0.15
Matches are distributed among these distances:
34 7 0.04
35 44 0.22
36 6 0.03
37 34 0.17
38 34 0.17
39 23 0.12
40 4 0.02
41 16 0.08
42 5 0.03
43 15 0.08
44 8 0.04
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTGAAAATATATATATTATATAGTTTTAAAAAACA
Found at i:305424 original size:74 final size:72
Alignment explanation
Indices: 305263--305442 Score: 195
Period size: 74 Copynumber: 2.5 Consensus size: 72
305253 TAAAAAGCAT
* * *
305263 TTTTGAAAACATATATATTATATAG-TTTTAAAAAAGCATTTTGAAATATATATAATATAGTTTT
1 TTTTGAAAAC-TATATAATATATGGTTTTTAAAAAAGCAGTTTGAAATATATATAATATAGTTTT
305327 CGAAAACA
65 CGAAAACA
* * *
305335 TTTTAAAAATGTATATAATATATGGTTTTTAAAAAA-CAGTTTGAAAAATATTTATAATATATAG
1 TTTTGAAAA-CTATATAATATATGGTTTTTAAAAAAGCAGTTTG--AAATATATAT-A-ATATAG
*
305399 TTTT-TAAAACA
61 TTTTCGAAAACA
* * *
305410 TTTTGAAAACTATATAGTATATGATTTTGAAAA
1 TTTTGAAAACTATATAATATATGGTTTTTAAAA
305443 CATTTCTTAG
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
72 26 0.29
73 10 0.11
74 29 0.32
75 15 0.17
76 10 0.11
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (72 bp):
TTTTGAAAACTATATAATATATGGTTTTTAAAAAAGCAGTTTGAAATATATATAATATAGTTTTC
GAAAACA
Found at i:305572 original size:6 final size:6
Alignment explanation
Indices: 305561--305598 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
305551 AAAATGTTCT
* *
305561 TTTTTA TTTTTA TTTTT- TATTTA TTTTTA TTATTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
305599 ATTTTTCAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:305596 original size:16 final size:17
Alignment explanation
Indices: 305563--305604 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
305553 AATGTTCTTT
*
305563 TTTATTTTTATTTTTTA
1 TTTATTTTTATTTATTA
305580 TTTATTTTTA-TTATTA
1 TTTATTTTTATTTATTA
305596 TTTATTTTT
1 TTTATTTTT
305605 CAGGTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTATTTATTA
Found at i:307111 original size:76 final size:73
Alignment explanation
Indices: 306952--307157 Score: 177
Period size: 76 Copynumber: 2.7 Consensus size: 73
306942 CATTTTGAAA
* *
306952 TATATAA-ATATAGTTTTCAAAAACATTTTAAAAATGTATATAATATATGCTTTTTAAAAAACAA
1 TATATAATATATAGTTTT-TAAAACATTTTAAAAA--TATATAATATATG-ATTTTAAAAAACAA
307016 TTTGAAAAATAT
62 TTTGAAAAATAT
* * * *
307028 T-TATAATATATAGTTTTTAAAACATTTTGAAAACTATATAGTATATGATTTT-GAAAACATTTC
1 TATATAATATATAGTTTTTAAAACATTTT-AAAAATATATAATATATGATTTTAAAAAACAATT-
* *
307091 TTAGAAAGTAT
64 TGA-AAAATAT
* * * * *
307102 GTATATAATATATA-ATTTTAAAATACTATTTCAAAATATATATTATAAGATTTTAA
1 -TATATAATATATAGTTTTTAAAACA-T-TTTAAAAATATATAATATATGATTTTAA
307158 TTTTTTTTAA
Statistics
Matches: 106, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
72 8 0.08
73 6 0.06
74 18 0.17
75 25 0.24
76 46 0.43
77 3 0.03
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (73 bp):
TATATAATATATAGTTTTTAAAACATTTTAAAAATATATAATATATGATTTTAAAAAACAATTTG
AAAAATAT
Found at i:307214 original size:6 final size:6
Alignment explanation
Indices: 307203--307240 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
307193 AAAATGTTCT
* *
307203 TTTTTA TTTTTA TTTTT- TATTTA TTTTTA TTATTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
307241 ATTTTTCAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:307238 original size:16 final size:17
Alignment explanation
Indices: 307205--307246 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
307195 AATGTTCTTT
*
307205 TTTATTTTTATTTTTTA
1 TTTATTTTTATTTATTA
307222 TTTATTTTTA-TTATTA
1 TTTATTTTTATTTATTA
307238 TTTATTTTT
1 TTTATTTTT
307247 CAGGTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTATTTATTA
Found at i:308199 original size:9 final size:9
Alignment explanation
Indices: 308185--308209 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
308175 TTACAACCCT
308185 CTCTCTCTC
1 CTCTCTCTC
308194 CTCTCTCTC
1 CTCTCTCTC
308203 CTCTCTC
1 CTCTCTC
308210 GTCTTAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
CTCTCTCTC
Found at i:308310 original size:26 final size:26
Alignment explanation
Indices: 308280--308346 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
308270 ATGTATTGCA
* *
308280 AAACGATGTAGTTTTTCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
308306 AAACGACGTAGTTTTGCCACTGCAAG
1 AAACGACGTAGTTTTGCCACTGCAAG
*
308332 AAATGACGTAGTTTT
1 AAACGACGTAGTTTT
308347 ATCCCATAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (26 bp):
AAACGACGTAGTTTTGCCACTGCAAG
Found at i:308512 original size:4 final size:4
Alignment explanation
Indices: 308503--308544 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
308493 CACTTTCTGC
* * *
308503 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
308545 TTTTGTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:308690 original size:15 final size:17
Alignment explanation
Indices: 308672--308707 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
308662 TTATTATTAT
308672 TTTTA-TTTTACT-AAA
1 TTTTATTTTTACTAAAA
308687 TTTTATTTTTACTAAAA
1 TTTTATTTTTACTAAAA
308704 TTTT
1 TTTT
308708 TCCCTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 7 0.37
17 7 0.37
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTTTTACTAAAA
Found at i:308692 original size:24 final size:22
Alignment explanation
Indices: 308641--308696 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
308631 TTCATTTGGA
*
308641 TTTATTTTTTTATTTACATTAT
1 TTTATTTTTTTATTTACATAAT
308663 TATTATTATTTTTATTTTAC-TAAAT
1 T-TTATT-TTTTTA-TTTACAT-AAT
308688 TTTATTTTT
1 TTTATTTTT
308697 ACTAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 12 0.41
25 8 0.28
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATTTTTTTATTTACATAAT
Found at i:309381 original size:37 final size:34
Alignment explanation
Indices: 309340--309424 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 34
309330 AGATATATAT
*
309340 TATATAGGTTTTTTTAAAAAACATTTTTGAAAACATA
1 TATATA-GTTTTTTAAAAAAACA-TTTTG-AAACATA
*
309377 TATATTA-TATAGTTTTAAAAAAACATTTTGAAATATA
1 TATA-TAGT-T--TTTTAAAAAAACATTTTGAAACATA
309414 TATATAGTTTT
1 TATATAGTTTT
309425 GAAAACATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
34 2 0.05
36 4 0.10
37 16 0.39
38 7 0.17
39 12 0.29
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (34 bp):
TATATAGTTTTTTAAAAAAACATTTTGAAACATA
Found at i:309417 original size:39 final size:42
Alignment explanation
Indices: 309320--309419 Score: 136
Period size: 39 Copynumber: 2.5 Consensus size: 42
309310 ATGCTAATGG
* *
309320 TTTTTGAAATAGATATATATTATATAGGTTTTTTTAAAAAACA
1 TTTTTGAAATACATATATATTATATAGG-TTTTTAAAAAAACA
309363 TTTTTGAAA-ACATATATATTATATA-G-TTTTAAAAAAACA
1 TTTTTGAAATACATATATATTATATAGGTTTTTAAAAAAACA
*
309402 -TTTTGAAATATATATATA
1 TTTTTGAAATACATATATA
309420 GTTTTGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
38 8 0.15
39 20 0.38
41 1 0.02
42 15 0.28
43 9 0.17
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (42 bp):
TTTTTGAAATACATATATATTATATAGGTTTTTAAAAAAACA
Found at i:309503 original size:37 final size:34
Alignment explanation
Indices: 309413--309513 Score: 112
Period size: 37 Copynumber: 2.8 Consensus size: 34
309403 TTTGAAATAT
* *
309413 ATATATAGTTTTGAAAACATTTTAAAAAAGTATA
1 ATATATAGTTTTTAAAACATTTGAAAAAAGTATA
* *
309447 ATATATGGTTTTTAAAAAACAGTTTGAAAAATATTTATA
1 ATATATAGTTTTT--AAAACA-TTTGAAAAA-A-GTATA
309486 ATATATAGTTTTTAAAACATTTTGAAAA
1 ATATATAGTTTTTAAAACA-TTTGAAAA
309514 CTATATAGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
34 11 0.20
36 6 0.11
37 22 0.39
38 1 0.02
39 16 0.29
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.41
Consensus pattern (34 bp):
ATATATAGTTTTTAAAACATTTGAAAAAAGTATA
Found at i:310933 original size:4 final size:4
Alignment explanation
Indices: 310924--310958 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
310914 TCCTTTCTAC
* *
310924 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
310959 ATATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:310944 original size:20 final size:20
Alignment explanation
Indices: 310919--310958 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
310909 TTTAGTCCTT
310919 TCTACTTATTTATTTATTTA
1 TCTACTTATTTATTTATTTA
310939 TCTACTTATTTATTTATTTA
1 TCTACTTATTTATTTATTTA
310959 ATATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (20 bp):
TCTACTTATTTATTTATTTA
Found at i:311537 original size:74 final size:71
Alignment explanation
Indices: 311367--311547 Score: 177
Period size: 74 Copynumber: 2.5 Consensus size: 71
311357 TAAAAAGCAT
* *
311367 TTTTGAAAACATATATATTATATAGTTTTTAAAAAAACATTTTGAAATATATATAATATAGTTTT
1 TTTTGAAAAC-TATATAATATAT-GTTTTTAAAAAAACAGTTTGAAATATATATAATATAGTTTT
311432 CGAAAACA
64 CGAAAACA
* * * * *
311440 TTTT-ATAAATGTATGTAAAATATGTTTTTTAAAAAACAGTTTGAAAAATATTTATAATATATAG
1 TTTTGA-AAA-CTATATAATATATGTTTTTAAAAAAACAGTTTG--AAATATATAT-A-ATATAG
*
311504 TTTT-TAAAACA
60 TTTTCGAAAACA
* * *
311515 TTTTGAAAACTATATAGTATATGATTTTGAAAA
1 TTTTGAAAACTATATAATATATGTTTTTAAAAA
311548 CATTTTTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
72 19 0.22
73 16 0.18
74 27 0.31
75 14 0.16
76 11 0.13
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (71 bp):
TTTTGAAAACTATATAATATATGTTTTTAAAAAAACAGTTTGAAATATATATAATATAGTTTTCG
AAAACA
Found at i:311644 original size:35 final size:33
Alignment explanation
Indices: 311549--311650 Score: 93
Period size: 33 Copynumber: 3.0 Consensus size: 33
311539 TTTTGAAAAC
*
311549 ATTTTTTTAGAAAGTATGTATATAATATAT-TTTTA
1 ATTTTTTTA-AAA--ATATATATAATATATATTTTA
* *
311584 ATATTATTTGAAAATATATAT--TATATGATTTTA
1 AT-TTTTTTAAAAATATATATAATATAT-ATTTTA
311617 ATTTTTTTAAAACATATATATAATATATTATTTT
1 ATTTTTTTAAAA-ATATATATAATATA-TATTTT
311651 TAAAATGTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
31 5 0.09
32 8 0.15
33 22 0.40
35 14 0.25
36 6 0.11
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (33 bp):
ATTTTTTTAAAAATATATATAATATATATTTTA
Found at i:313071 original size:3 final size:3
Alignment explanation
Indices: 313065--313104 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
313055 TTTTATTTCC
313065 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
313105 CTAAATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:313692 original size:2 final size:2
Alignment explanation
Indices: 313685--313733 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
313675 TCGTCCGTAT
313685 TA TA TA TA TA TA TA TA -A 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
313726 TA TA TA TA
1 TA TA TA TA
313734 CTAATGGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:313820 original size:41 final size:42
Alignment explanation
Indices: 313741--313839 Score: 123
Period size: 41 Copynumber: 2.4 Consensus size: 42
313731 ATACTAATGG
* **
313741 TTTTTGAAATAGATATATATTATATAGGTTTTTTAAAAAGAA
1 TTTTTGAAATACATATATATTATATAGGTTTTAAAAAAAGAA
313783 TTTTTGAAA-ACATATATATTATATA-GTTTTAAAAAAA-AA
1 TTTTTGAAATACATATATATTATATAGGTTTTAAAAAAAGAA
* *
313822 CATTTTGAAATATATATA
1 -TTTTTGAAATACATATA
313840 AAATAGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
39 2 0.04
40 18 0.36
41 21 0.42
42 9 0.18
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.43
Consensus pattern (42 bp):
TTTTTGAAATACATATATATTATATAGGTTTTAAAAAAAGAA
Found at i:313837 original size:39 final size:40
Alignment explanation
Indices: 313742--313839 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 40
313732 TACTAATGGT
* * *
313742 TTTTGAAATAGATATATATTATATAGGTTTTTTAAAAAGAAT
1 TTTTGAAAT--ATATATATTATATAGGTTTTTAAAAAAAAAA
*
313784 TTTTGAAAACATATATATTATATA-G-TTTTAAAAAAAAACA
1 TTTTG-AAATATATATATTATATAGGTTTTTAAAAAAAAA-A
313824 TTTTGAAATATATATA
1 TTTTGAAATATATATA
313840 AAATAGTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
39 21 0.43
40 6 0.12
41 14 0.29
42 5 0.10
43 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (40 bp):
TTTTGAAATATATATATTATATAGGTTTTTAAAAAAAAAA
Found at i:313892 original size:74 final size:73
Alignment explanation
Indices: 313797--313939 Score: 166
Period size: 74 Copynumber: 1.9 Consensus size: 73
313787 TGAAAACATA
*
313797 TATATTATATAGTTTTAAAAAAAAACAT-TTTG-AAATATAT-ATAAAATAGTTTTCGAAAACAT
1 TATAATATATAGTTTT--AAAAAAAC-TGTTTGAAAATATATAATAAAATAGTTTT-GAAAACAT
313859 TTTAAAAATGTG
62 TTTAAAAATGTG
* * * * * *
313871 TATAATATATGGTTTTTAAAAAACTGTTTGAAAATATTTAATATAATAGTTTTTAAAACATTTTG
1 TATAATATATAGTTTTAAAAAAACTGTTTGAAAATATATAATAAAATAGTTTTGAAAACATTTTA
313936 AAAA
66 AAAA
313940 CTATATAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
71 1 0.02
72 11 0.19
73 21 0.36
74 26 0.44
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (73 bp):
TATAATATATAGTTTTAAAAAAACTGTTTGAAAATATATAATAAAATAGTTTTGAAAACATTTTA
AAAATGTG
Found at i:313964 original size:35 final size:34
Alignment explanation
Indices: 313817--314037 Score: 128
Period size: 35 Copynumber: 6.1 Consensus size: 34
313807 AGTTTTAAAA
*
313817 AAAAACATTTTGAAATATATATAAAATA-G-TTTT
1 AAAAACATTTTGAAA-ATATATAATATATGATTTT
* * * *
313850 CGAAAACATTTTAAAAATGTGTATAATATATGGTTTTT
1 -AAAAACATTTTGAAAA--TATATAATATAT-GATTTT
*
313888 AAAAA-ACTGTTTGAAAATATTTAATATAAT-AGTTTT
1 AAAAACA-T-TTTGAAAATATATAATAT-ATGA-TTTT
* *
313924 TAAAACATTTTGAAAACTATATAGTATATGATTTT
1 AAAAACATTTTGAAAA-TATATAATATATGATTTT
*
313959 AAAAACATTTGTTTAGAAAGTATGTATATAATATATAATTTT
1 AAAAACA--T-TTT-GAAA--A--TATATAATATATGATTTT
* *
314001 AAAATATTATTTT-AAAATATATATTATATGATTTT
1 AAAA-A-CATTTTGAAAATATATAATATATGATTTT
314036 AA
1 AA
314038 TTTTTTTTTA
Statistics
Matches: 147, Mismatches: 19, Indels: 41
0.71 0.09 0.20
Matches are distributed among these distances:
33 1 0.01
34 13 0.09
35 47 0.32
36 27 0.18
37 11 0.07
38 14 0.10
39 7 0.05
41 4 0.03
42 21 0.14
43 1 0.01
44 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (34 bp):
AAAAACATTTTGAAAATATATAATATATGATTTT
Found at i:314012 original size:13 final size:13
Alignment explanation
Indices: 313991--314025 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
313981 TGTATATAAT
*
313991 ATATAATTTTAAA
1 ATATTATTTTAAA
314004 ATATTATTTTAAA
1 ATATTATTTTAAA
314017 ATATATATT
1 ATAT-TATT
314026 ATATGATTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTATTTTAAA
Found at i:314104 original size:12 final size:12
Alignment explanation
Indices: 314087--314125 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
314077 AATGTTCTTT
314087 TTTATTTTTATA
1 TTTATTTTTATA
314099 TTTATTTTTTATA
1 TTTA-TTTTTATA
*
314112 TTTATTTTTTTA
1 TTTATTTTTATA
314124 TT
1 TT
314126 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTATA
Found at i:314120 original size:14 final size:13
Alignment explanation
Indices: 314087--314125 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
314077 AATGTTCTTT
314087 TTTA-TTTTTATA
1 TTTATTTTTTATA
314099 TTTATTTTTTATA
1 TTTATTTTTTATA
314112 TTTATTTTTT-TA
1 TTTATTTTTTATA
314124 TT
1 TT
314126 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTATA
Found at i:315084 original size:12 final size:12
Alignment explanation
Indices: 315067--315096 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
315057 TTGAGAGAGT
315067 CTCTCTCCTCTC
1 CTCTCTCCTCTC
315079 CTCTCTCCTCTC
1 CTCTCTCCTCTC
315091 CTCTCT
1 CTCTCT
315097 TCGTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCTCTCCTCTC
Found at i:315533 original size:27 final size:24
Alignment explanation
Indices: 315470--315537 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 24
315460 ATATCTAACC
*
315470 TTTTTAGTTTTTTATTTCATTTAG
1 TTTTTATTTTTTTATTTCATTTAG
* *
315494 ATTTTATTTTTTTATTTCCATTATTAT
1 TTTTTATTTTTTTATTT-CA-T-TTAG
315521 TTTTTATTTTTTTATTT
1 TTTTTATTTTTTTATTT
315538 TTACTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 15 0.41
25 2 0.05
26 1 0.03
27 19 0.51
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTTTATTTTTTTATTTCATTTAG
Found at i:315549 original size:24 final size:25
Alignment explanation
Indices: 315471--315554 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 25
315461 TATCTAACCT
* *
315471 TTTTAGTTTTTTATTTCATT--TAGA
1 TTTTATTTTTTTATTTC-TTACTAAA
* **
315495 TTTTATTTTTTTATTTCCATTATTATT
1 TTTTATTTTTTTATTT-C-TTACTAAA
315522 TTTTATTTTTTTATTT-TTACTAAA
1 TTTTATTTTTTTATTTCTTACTAAA
315546 TTTTATTTT
1 TTTTATTTT
315555 CCCTATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
24 29 0.57
25 4 0.08
27 18 0.35
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTATTTTTTTATTTCTTACTAAA
Found at i:315619 original size:18 final size:18
Alignment explanation
Indices: 315585--315618 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
315575 TGATATATTT
315585 TCTTACTTATTTATTTTA
1 TCTTACTTATTTATTTTA
*
315603 TCTTCCTTATTT-TTTT
1 TCTTACTTATTTATTTT
315619 TTTTCTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTACTTATTTATTTTA
Found at i:315726 original size:23 final size:22
Alignment explanation
Indices: 315673--315731 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
315663 TGACTTTGTT
*
315673 TTATTATTTTTTTGGTTATTATG
1 TTATTATTTTTTTAGTTATTA-G
*
315696 TTAGTATTTTATTTAGTTAATTA-
1 TTATTATTTT-TTTAGTT-ATTAG
*
315719 TTATTATTATTTT
1 TTATTATTTTTTT
315732 GATTTTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 3 0.10
23 17 0.57
24 6 0.20
25 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (22 bp):
TTATTATTTTTTTAGTTATTAG
Found at i:321155 original size:164 final size:163
Alignment explanation
Indices: 320781--321337 Score: 555
Period size: 164 Copynumber: 3.4 Consensus size: 163
320771 TTTAAGATAA
* * * *
320781 CATTTGCATCATAACTCATGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAATTCGACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGCC--CAAAGACCTTCGAGTTCGACTACG
* * *
320846 CTCAGCTCCAAGGCGCATAATTTACAGCATAACTTT-AGTCGAGAAGGGCTATCTG--CCAAAGA
64 CTCAGCTCCAAGGCACATCATTTACAGCATAA-TTTAAGTCGAGAAGGGTTATCTGCACCAAAGA
* * * * **
320908 CCCTCGAGTTTGACTATGCTCAGCTATAAGGGCACAT
128 CCTTCGAGTTCGACTACGCTCAACTCCAA-GGCACAT
* * *
320945 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTG-C-CCAAAGACCTTCGAGTTCGACTACG
* * * * *
321010 CTCAACTCCAAGGCATATCATTTGCAGCATAATTTAAATCGAGAAGGGTTATATGCCAACCAAAG
64 CTCAGCTCCAAGGCACATCATTTACAGCATAATTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAG
**
321075 ACCTTCGAGTTCGACTACGCTCAACTCCAAGGCGTAT
127 ACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACAT
* * * * * * * *
321112 CATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGATTACACT
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGACTACGCT
** * * * * * *
321176 CAGCTTTGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCGAAAGA
66 CAGC-TCCAAGGCACATCATTTACAGCATAATTTAAGTCGAGAAGGGTTATCTG-CACC-AAAGA
321241 CCTTCGAGTTCGACTACGCTCAACTCCAAGGCACAT
128 CCTTCGAGTTCGACTACGCTCAACTCCAAGGCACAT
* * * * * *
321277 CATTTGTAGCATATCTTAAGTCAAGAAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGA
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTG-C--CCAAAGACCTTCGAGTTCGA
321338 TTACACTCGG
Statistics
Matches: 326, Mismatches: 54, Indels: 21
0.81 0.13 0.05
Matches are distributed among these distances:
163 3 0.01
164 128 0.39
165 111 0.34
166 1 0.00
167 35 0.11
168 30 0.09
169 18 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (163 bp):
CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTACAGCATAATTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCT
TCGAGTTCGACTACGCTCAACTCCAAGGCACAT
Found at i:321218 original size:248 final size:249
Alignment explanation
Indices: 320804--321337 Score: 831
Period size: 248 Copynumber: 2.2 Consensus size: 249
320794 ACTCATGGCT
* *
320804 AGAAGGGTTATCTGCCAA-CAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCGCATAATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCGCATAATT
* * **
320868 TACAGCATAACTTTAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGACTATGCTCAGCT
66 TACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCT
*
320933 ATAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTC
131 ATAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCGAAAGACCTTC
* *
320997 GAGTTCAACTACGCTCAACTCCAAGGCATATCATTTGCAGCATAAT-TTAAATCG
196 GAGTTCAACTACGCTCAACTCCAAGGCACATCATTTGCAGCAT-ATCTTAAATCA
* * *
321051 AGAAGGGTTATATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCGTATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCGCATAATT
* * * *
321116 TGCATCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
66 TACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCT
* *
321181 TTGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCGAAAGACCTTC
131 ATAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCGAAAGACCTTC
* * *
321246 GAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGTAGCATATCTTAAGTCA
196 GAGTTCAACTACGCTCAACTCCAAGGCACATCATTTGCAGCATATCTTAAATCA
* *
321300 AGAAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGA
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
321338 TTACACTCGG
Statistics
Matches: 260, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
247 17 0.07
248 152 0.58
249 91 0.35
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (249 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCGCATAATT
TACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCT
ATAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCGAAAGACCTTC
GAGTTCAACTACGCTCAACTCCAAGGCACATCATTTGCAGCATATCTTAAATCA
Found at i:321357 original size:84 final size:83
Alignment explanation
Indices: 320804--321337 Score: 558
Period size: 84 Copynumber: 6.4 Consensus size: 83
320794 ACTCATGGCT
* * * *
320804 AGAAGGGTTATCTGCCAACAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCGCATAATTT
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
320869 ACAGCATAACTTTAGTCG
66 ACAGCATAACTTAAGTCG
* * * * **
320887 AGAAGGGCTATCTG---CCAAAGACCCTCGAGTTTGACTATGCTCAGCTATAAGGGCACATCATT
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATT
* * *
320949 TACAGCATAACTCAAGGCT
65 TACAGCATAACTTAAGTCG
* * * *
320968 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTACGCTCAACTCCAAGGCATATCATTT
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
321033 GCAGCATAATTTAAATCG
66 ACAGCATAACTTAAGTCG
* * **
321051 AGAAGGGTTATATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCGTATCATT
1 AGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
321116 TGCATCATAGCTTAAGTCG
65 TACAGCATAACTTAAGTCG
* * * * ** *
321135 AGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATT
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
* * * *
321197 TACAACATAACTCAAGGCT
65 TACAGCATAACTTAAGTCG
* *
321216 AGAAGGGTTATCTGTCACCGAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
** * *
321281 TGTAGCATATCTTAAGTCA
65 TACAGCATAACTTAAGTCG
* *
321300 AGAAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGA
1 AGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
321338 TTACACTCGG
Statistics
Matches: 368, Mismatches: 72, Indels: 21
0.80 0.16 0.05
Matches are distributed among these distances:
80 56 0.15
81 74 0.20
83 50 0.14
84 160 0.43
85 28 0.08
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
ACAGCATAACTTAAGTCG
Found at i:322021 original size:34 final size:34
Alignment explanation
Indices: 321983--322153 Score: 100
Period size: 34 Copynumber: 4.8 Consensus size: 34
321973 ATATAGGTTT
*
321983 TTTTAAAAAAGTATTTTTGAAA-ACATAT-ATATAG
1 TTTTAAAAAA-CA-TTTTGAAATACATATAATATAG
*
322017 TTTTAAAAAACATTTTGAAATATATATAATATAG
1 TTTTAAAAAACATTTTGAAATACATATAATATAG
** * **
322051 TTTTCGAAAACATTTTAAAAATGTATATAATATATGG
1 TTTTAAAAAACATTTT-GAAATACATATAATATA--G
* **
322088 CTTTTAAAAATA-AGTTTGAAAAATATTTATAATATATAG
1 -TTTTAAAAA-ACATTTTG--AAATACATAT-A-ATATAG
*
322127 TTTT-TAAAACATTTTGAAA-ACTATATA
1 TTTTAAAAAACATTTTGAAATAC-ATATA
322154 GTACATTATT
Statistics
Matches: 108, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
32 8 0.07
33 6 0.06
34 32 0.30
35 21 0.19
36 1 0.01
37 9 0.08
38 15 0.14
39 10 0.09
40 1 0.01
41 5 0.05
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (34 bp):
TTTTAAAAAACATTTTGAAATACATATAATATAG
Found at i:322195 original size:76 final size:71
Alignment explanation
Indices: 322106--322281 Score: 171
Period size: 76 Copynumber: 2.4 Consensus size: 71
322096 AATAAGTTTG
*
322106 AAAA-ATATTTATAATATATAGTTTTTAAAACA-T-TTTGAAAACTATATAGTACATTATTTTGA
1 AAAACATATATATAATATATAGTTTTTAAAACATTATTTGAAAA-TATATAGTACATTATTTT--
322168 AAACATTTTTT
63 -AA-ATTTTTT
* * * * * * *
322179 AGAAAGTATGTATATAATATATA-ATTTTAAAATATTATTTGAAAATGTATATTATATTATTTTA
1 A-AAA-CATATATATAATATATAGTTTTTAAAACATTATTTGAAAATATATAGTACATTATTTTA
*
322243 ATTTTTTT
64 AATTTTTT
*
322251 AAAACATATATATAATATATTGTTTTTAAAA
1 AAAACATATATATAATATATAGTTTTTAAAA
322282 TGTTCTTTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
70 14 0.16
71 11 0.13
72 7 0.08
73 3 0.04
74 3 0.04
75 9 0.11
76 30 0.35
77 8 0.09
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (71 bp):
AAAACATATATATAATATATAGTTTTTAAAACATTATTTGAAAATATATAGTACATTATTTTAAA
TTTTTT
Found at i:323551 original size:4 final size:4
Alignment explanation
Indices: 323542--323575 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
323532 CACTTTCTTC
* *
323542 TTAT TTAT TTAT TTAT CTAC TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
323576 CTATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:323582 original size:16 final size:15
Alignment explanation
Indices: 323546--323593 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
323536 TTCTTCTTAT
*
323546 TTATTTATTTATCTAC
1 TTATTTATTTAT-TTC
323562 TTATTTATTTATTTC
1 TTATTTATTTATTTC
*
323577 TATATTT-TTTGTTTC
1 T-TATTTATTTATTTC
323592 TT
1 TT
323594 TTGGTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 17 0.59
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTATTTATTTC
Found at i:326559 original size:30 final size:29
Alignment explanation
Indices: 326520--326593 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
326510 AATGTCCTTG
* *
326520 AGCTTCCATGAGCTGCCAAAGAGATAGTA
1 AGCTTCCATGAGCTACCAAAGAAATAGTA
*
326549 AGCTATCCATGAGCTACCAAAGAAATAGTG
1 AGCT-TCCATGAGCTACCAAAGAAATAGTA
*
326579 AGCTTTCCATAAGCT
1 AGC-TTCCATGAGCT
326594 TCCATATGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 4 0.10
30 34 0.87
31 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (29 bp):
AGCTTCCATGAGCTACCAAAGAAATAGTA
Found at i:328659 original size:30 final size:30
Alignment explanation
Indices: 328620--328684 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
328610 AGAGAGAGTG
* * * *
328620 AGCTATCCATGAGTTGCCATATGCCTTCCT
1 AGCTTTCCATGAGCTACCATATGCCTTCCC
328650 AGCTTTCCATGAGCTACCATATGCCTTCCC
1 AGCTTTCCATGAGCTACCATATGCCTTCCC
328680 AGCTT
1 AGCTT
328685 GTCAAGCACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.32, G:0.15, T:0.32
Consensus pattern (30 bp):
AGCTTTCCATGAGCTACCATATGCCTTCCC
Found at i:329461 original size:213 final size:211
Alignment explanation
Indices: 329095--329508 Score: 623
Period size: 212 Copynumber: 2.0 Consensus size: 211
329085 AAAACTTATT
* * **
329095 ATTTTTATCAACACAGATTAATTCCATTTACTTATGCACATAAGAATAATTTTGTAATTTCAACA
1 ATTTTTATCAACACAGATTAATTCCATTCACTTATGCACATAAGAACAATTCAGTAATTTCAACA
* * * *
329160 CTCTAAGGACATCTTAGTACTCTAACACACTTATAGTATATCAGACTTATTAAAGCTTAGTAAAA
66 CTCTAAGGACATCTTAGTAATCTAACACACTCAAAGTATATAAGACTTATTAAAGCTTAGTAAAA
* * *
329225 TAGTATTACCTTAATTATCAGTGTTTTAATACCCTTTTTTTACACTCTTAGACTTTTGTTATCAC
131 TAGTATTAACTTAATTATCAGTGTTTTAATA-CCTTTTTTTACACTCTTAGACTTTTCTTATCAA
329290 TTATTATGACTAAGTGC
195 TTATTATGACTAAGTGC
* *
329307 ATTTTTATCAACATAGATT-ATTCCATTCACTTATGCACATAAGGACAATTCAGTAATTTCAACC
1 ATTTTTATCAACACAGATTAATTCCATTCACTTATGCACATAAGAACAATTCAGTAATTTCAA-C
* * * * *
329371 TCTCTAAGGACATTTTAGTAATTTGACACACTCACAAGTATATAAGACTTATTAAAGCTTATTAA
65 ACTCTAAGGACATCTTAGTAATCTAACACACTCA-AAGTATATAAGACTTATTAAAGCTTAGTAA
*
329436 AATAGTATTAACTTAATTATCAGTGTTTTAATACCTTTTTTTACACTCTTAGGCTTTTCTTATCA
129 AATAGTATTAACTTAATTATCAGTGTTTTAATACCTTTTTTTACACTCTTAGACTTTTCTTATCA
329501 ATTATTAT
194 ATTATTAT
329509 CATTAAGGGT
Statistics
Matches: 181, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
211 38 0.21
212 84 0.46
213 59 0.33
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.41
Consensus pattern (211 bp):
ATTTTTATCAACACAGATTAATTCCATTCACTTATGCACATAAGAACAATTCAGTAATTTCAACA
CTCTAAGGACATCTTAGTAATCTAACACACTCAAAGTATATAAGACTTATTAAAGCTTAGTAAAA
TAGTATTAACTTAATTATCAGTGTTTTAATACCTTTTTTTACACTCTTAGACTTTTCTTATCAAT
TATTATGACTAAGTGC
Found at i:329988 original size:18 final size:17
Alignment explanation
Indices: 329965--329998 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
329955 CAATACAATA
*
329965 ATATTATTTTTTGATATT
1 ATATTATATTTT-ATATT
329983 ATATTATATTTTATAT
1 ATATTATATTTTATAT
329999 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:331909 original size:19 final size:19
Alignment explanation
Indices: 331856--331909 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
331846 CCTTGTTTTC
331856 ATTTTTTATTTT-ATTACT
1 ATTTTTTATTTTAATTACT
331874 ATTTTTTATTTTAAATTA-T
1 ATTTTTTATTTT-AATTACT
*
331893 ATTTTTCATTTATAATT
1 ATTTTTTATTT-TAATT
331910 TCAAAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 12 0.38
19 15 0.47
20 5 0.16
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTTTATTTTAATTACT
Found at i:332048 original size:5 final size:5
Alignment explanation
Indices: 332038--332089 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
332028 TAATTTTATA
* *
332038 ATTTT ATTTT ATTTT -TTGT ATTTT ATAATTT ATTTT ATTTT -TTGT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT--TTT ATTTT ATTTT ATTTT ATTTT
332088 AT
1 AT
332090 AATTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
7 5 0.13
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:332061 original size:7 final size:7
Alignment explanation
Indices: 332030--332141 Score: 63
Period size: 7 Copynumber: 16.4 Consensus size: 7
332020 TTTAATTCTA
332030 ATTTTAT
1 ATTTTAT
*
332037 AATTT-T
1 ATTTTAT
332043 ATTTTAT
1 ATTTTAT
* *
332050 TTTTTGT
1 ATTTTAT
332057 ATTTTAT
1 ATTTTAT
*
332064 A-ATT-T
1 ATTTTAT
332069 ATTTTAT
1 ATTTTAT
* *
332076 TTTTTGT
1 ATTTTAT
332083 ATTTTAT
1 ATTTTAT
332090 AATTTTAT
1 -ATTTTAT
*
332098 -TTTTAG
1 ATTTTAT
*
332104 ATTATAT
1 ATTTTAT
* *
332111 AATTTAA
1 ATTTTAT
*
332118 ATTTATAA
1 ATTT-TAT
332126 ATTTTAT
1 ATTTTAT
*
332133 -GTTTAT
1 ATTTTAT
332139 ATT
1 ATT
332142 ATGTATTATA
Statistics
Matches: 76, Mismatches: 22, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
5 2 0.03
6 19 0.25
7 41 0.54
8 14 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:332071 original size:21 final size:22
Alignment explanation
Indices: 332043--332115 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 22
332033 TTATAATTTT
332043 ATTTTATTTTTTGTATTTTATAA
1 ATTTTATTTTTTGTATTTTAT-A
332066 TTTATTTTATTTTTTGTATTTTATA
1 ---ATTTTATTTTTTGTATTTTATA
* *
332091 ATTTTATTTTTAG-ATTATATA
1 ATTTTATTTTTTGTATTTTATA
332112 ATTT
1 ATTT
332116 AAATTTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
21 11 0.24
22 12 0.27
25 1 0.02
26 21 0.47
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTATTTTTTGTATTTTATA
Found at i:332076 original size:26 final size:27
Alignment explanation
Indices: 332030--332100 Score: 135
Period size: 26 Copynumber: 2.7 Consensus size: 27
332020 TTTAATTCTA
332030 ATTTTATAATTTTATTTTATTTTTTGT
1 ATTTTATAATTTTATTTTATTTTTTGT
332057 ATTTTATAA-TTTATTTTATTTTTTGT
1 ATTTTATAATTTTATTTTATTTTTTGT
332083 ATTTTATAATTTTATTTT
1 ATTTTATAATTTTATTTT
332101 TAGATTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 26 0.60
27 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (27 bp):
ATTTTATAATTTTATTTTATTTTTTGT
Found at i:339277 original size:25 final size:25
Alignment explanation
Indices: 339249--339304 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
339239 AAAACAGAAG
339249 ATAAAATTTTAGTTTAGAGAAAGGT
1 ATAAAATTTTAGTTTAGAGAAAGGT
339274 ATAAAATTTTAGTTTAGAGAAAGGT
1 ATAAAATTTTAGTTTAGAGAAAGGT
339299 A-AAAAT
1 ATAAAAT
339305 AAATTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (25 bp):
ATAAAATTTTAGTTTAGAGAAAGGT
Found at i:340416 original size:21 final size:21
Alignment explanation
Indices: 340390--340436 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
340380 GGCTTTGGAA
*
340390 TTTTCCTGAGATATAACCAGC
1 TTTTCCTGAGATATAACCAAC
* *
340411 TTTTCCTGGGATGTAACCAAC
1 TTTTCCTGAGATATAACCAAC
340432 TTTTC
1 TTTTC
340437 TTGTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TTTTCCTGAGATATAACCAAC
Found at i:341153 original size:19 final size:20
Alignment explanation
Indices: 341112--341162 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
341102 GAAACCCCTT
*
341112 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
341132 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
341151 TGAAGATACATG
1 TGAAAATACATG
341163 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:346616 original size:13 final size:12
Alignment explanation
Indices: 346597--346646 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
346587 AATTGTTTTG
346597 AAATAAAAAATA
1 AAATAAAAAATA
346609 AGAAT--AAAATA
1 A-AATAAAAAATA
*
346620 AAATATAAAGATA
1 AAATA-AAAAATA
346633 AAATAAATAAATA
1 AAATAAA-AAATA
346646 A
1 A
346647 TTAAAGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 3 0.10
13 18 0.58
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:346618 original size:18 final size:18
Alignment explanation
Indices: 346597--346646 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
346587 AATTGTTTTG
346597 AAATAAAAAAT-AAGAATA
1 AAATAAAAAATAAAG-ATA
*
346615 AAATAAAATATAAAGATA
1 AAATAAAAAATAAAGATA
346633 AAATAAATAAATAA
1 AAATAAA-AAATAA
346647 TTAAAGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAAGATA
Found at i:348142 original size:3 final size:3
Alignment explanation
Indices: 348134--348223 Score: 87
Period size: 3 Copynumber: 30.3 Consensus size: 3
348124 GATATTACTA
* *
348134 TAT TAT TAT TAC TAT TAT TAT ATAT AAT TA- TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
* * * *
348180 TAC TA- TAT TAT TGT TAT TAC TA- TAT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
348224 TACAATACTC
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 6 0.08
3 60 0.83
4 6 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:348188 original size:17 final size:17
Alignment explanation
Indices: 348126--348223 Score: 105
Period size: 17 Copynumber: 5.9 Consensus size: 17
348116 TCTGAGTTGA
348126 TATTACTATATTATTAT
1 TATTACTATATTATTAT
*
348143 TACTA-T-TATTATATAT
1 TATTACTATATTAT-TAT
* *
348159 AATTATATATATTATTAT
1 TATTA-CTATATTATTAT
*
348177 TATTACTATATTATTGT
1 TATTACTATATTATTAT
*
348194 TATTACTATATTATTGT
1 TATTACTATATTATTAT
348211 TATTA-T-TATTATT
1 TATTACTATATTATT
348224 TACAATACTC
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.18
16 8 0.11
17 36 0.51
18 8 0.11
19 6 0.08
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTACTATATTATTAT
Found at i:349179 original size:11 final size:11
Alignment explanation
Indices: 349163--349194 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
349153 TGTCTTCAAA
349163 TTTTATTTTAC
1 TTTTATTTTAC
349174 TTTTATTTTAC
1 TTTTATTTTAC
349185 TTTTATTTTA
1 TTTTATTTTA
349195 GTCACTGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTTAC
Found at i:349183 original size:16 final size:16
Alignment explanation
Indices: 349162--349194 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
349152 TTGTCTTCAA
349162 ATTTTATTTTACTTTT
1 ATTTTATTTTACTTTT
349178 ATTTTACTTTTA-TTTT
1 ATTTTA-TTTTACTTTT
349194 A
1 A
349195 GTCACTGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTATTTTACTTTT
Found at i:350694 original size:46 final size:47
Alignment explanation
Indices: 350604--350696 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
350594 GTATTACTAT
* * * *
350604 TTTATTTTCTAAATAAATGCATGCGAACTAGAAATCAAGCGGTTAGG
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCAAGAGGTTAGG
*
350651 TTTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTA-TTTTCCAAACAAATGCATGCGAACTAGAAAGCAAGAGGTTAGG
350697 ATATATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
46 20 0.50
47 9 0.22
48 11 0.28
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCAAGAGGTTAGG
Found at i:352037 original size:21 final size:21
Alignment explanation
Indices: 352011--352060 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
352001 GGTTTTGGAA
352011 TTTTCTTGGGATGCAACCAGC
1 TTTTCTTGGGATGCAACCAGC
* * *
352032 TTTTCTTCGGATGTAACCATC
1 TTTTCTTGGGATGCAACCAGC
352053 TTTTCTTG
1 TTTTCTTG
352061 TGAAATTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTTCTTGGGATGCAACCAGC
Found at i:355515 original size:21 final size:20
Alignment explanation
Indices: 355490--355528 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
355480 CTATTGCCAA
355490 TATTTTTATTTTCTATTTTTC
1 TATTTTTATTTTCT-TTTTTC
*
355511 TATTTTTCTTTTCTTTTT
1 TATTTTTATTTTCTTTTT
355529 GAGCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTATTTTCTTTTTTC
Found at i:356367 original size:13 final size:12
Alignment explanation
Indices: 356348--356398 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
356338 AATTGTTTTG
356348 AAATAAAAAATA
1 AAATAAAAAATA
356360 AGAAT--AAAATA
1 A-AATAAAAAATA
*
356371 AAATATAAAGATA
1 AAATA-AAAAATA
356384 AAATAAATAAATA
1 AAATAAA-AAATA
356397 AA
1 AA
356399 TAATTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.09
11 7 0.22
12 3 0.09
13 19 0.59
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:356369 original size:18 final size:18
Alignment explanation
Indices: 356348--356398 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
356338 AATTGTTTTG
356348 AAATAAAAAAT-AAGAATA
1 AAATAAAAAATAAAG-ATA
*
356366 AAATAAAATATAAAGATA
1 AAATAAAAAATAAAGATA
356384 AAATAAATAAATAAA
1 AAATAAA-AAATAAA
356399 TAATTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAAGATA
Found at i:357770 original size:8 final size:8
Alignment explanation
Indices: 357757--357815 Score: 55
Period size: 8 Copynumber: 6.5 Consensus size: 8
357747 TCTTCTGAGT
357757 TTATATTA
1 TTATATTA
357765 TTATATTA
1 TTATATTA
357773 TTATTACTGTTA
1 TTA-TA---TTA
357785 TTATATATAA
1 TTATAT-T-A
357795 TTATATATA
1 TTATAT-TA
357804 TTATATTA
1 TTATATTA
357812 TTAT
1 TTAT
357816 TTACAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
8 18 0.40
9 10 0.22
10 9 0.20
11 2 0.04
12 6 0.13
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (8 bp):
TTATATTA
Found at i:357805 original size:19 final size:18
Alignment explanation
Indices: 357757--357809 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
357747 TCTTCTGAGT
*
357757 TTATATTATTATATTATTA
1 TTATATTATTATA-TATAA
*
357776 TTACTGTTATTATATATAA
1 TTA-TATTATTATATATAA
357795 TTATATATATTATAT
1 TTATAT-TATTATAT
357810 TATTATTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 2 0.07
19 18 0.62
20 9 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTATATTATTATATATAA
Found at i:360280 original size:46 final size:47
Alignment explanation
Indices: 360195--360287 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
360185 GTATTATTAT
* *
360195 TTTATTTTCTAAATAAATGCATGCGAACTAGAAACCATGAGGTTAGG
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAACCATGAGGTTAGG
*
360242 TTTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTA-TTTTCCAAACAAATGCATGCGAACTAGAAACCATGAGGTTAGG
360288 ATATTGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 22 0.52
47 9 0.21
48 11 0.26
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGCATGCGAACTAGAAACCATGAGGTTAGG
Found at i:366479 original size:20 final size:20
Alignment explanation
Indices: 366451--366504 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
366441 TCTAGAAAAT
* * *
366451 TAAATCCTCCGGGTGATTTG
1 TAAAACCTCCGGGTCATCTG
366471 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTG
* *
366491 TAAAGCCTCAGGGT
1 TAAAACCTCCGGGT
366505 AGGATGTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTG
Found at i:366508 original size:119 final size:119
Alignment explanation
Indices: 366347--366856 Score: 831
Period size: 119 Copynumber: 4.3 Consensus size: 119
366337 ATTTCCATGA
* *
366347 ATTTATAAAGCCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
366412 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
*
366466 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGAATGAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
366531 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* * *
366585 ATTTGTAAAACCTCTGGGTCATCTATAAAGCCTTAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
* * *
366650 AACAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCTGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* * * *
366704 ATTTGTAAAACCTCCGGGCCATTTGTAAAGGCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
* * * * *
366769 AGCGATTTTCATAGTTTCTCATTTAACGTTCTAGAAAATTAAATCTTACGGGTT
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* * *
366823 ATTTGTAAAACCTCTGGGTCATTTGTAAAACCTC
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTC
366857 CAGGTCATTT
Statistics
Matches: 362, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 362 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (119 bp):
ATTTGTAAAACCTCCGGGTCATCTGTAAAGCCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
Found at i:366841 original size:20 final size:20
Alignment explanation
Indices: 366817--366921 Score: 165
Period size: 20 Copynumber: 5.2 Consensus size: 20
366807 TTAAATCTTA
*
366817 CGGGTTATTTGTAAAACCTC
1 CGGGTCATTTGTAAAACCTC
*
366837 TGGGTCATTTGTAAAACCTC
1 CGGGTCATTTGTAAAACCTC
*
366857 CAGGTCATTTGTAAAACCTC
1 CGGGTCATTTGTAAAACCTC
*
366877 CGGGTCATCTGTAAAACCTC
1 CGGGTCATTTGTAAAACCTC
*
366897 CGGGTCATATGTAAAACCTC
1 CGGGTCATTTGTAAAACCTC
366917 CGGGT
1 CGGGT
366922 AGGATGTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (20 bp):
CGGGTCATTTGTAAAACCTC
Found at i:367073 original size:3 final size:3
Alignment explanation
Indices: 367065--367140 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
367055 TTTGAGTTGA
* *
367065 TAT TAT TA- TAT TAT TAC TAT TAT TAT ATAT AAT TAT ATAT ATAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT -TAT TAT
*
367111 TAT TAT TAT TAT TAC TA- TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
367141 TACAAGACCC
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
2 6 0.10
3 47 0.75
4 10 0.16
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:367087 original size:14 final size:15
Alignment explanation
Indices: 367068--367138 Score: 73
Period size: 14 Copynumber: 4.9 Consensus size: 15
367058 GAGTTGATAT
367068 TATTA-TATTATTAC
1 TATTATTATTATTAC
367082 TATTATTA-TA-TA-
1 TATTATTATTATTAC
367094 TAATTATATATATATTA-
1 T-ATTAT-TAT-TATTAC
367111 TATTATTATTATTAC
1 TATTATTATTATTAC
367126 TA-TATTATTATTA
1 TATTATTATTATTA
367139 TTTACAAGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
12 1 0.02
13 7 0.14
14 25 0.50
15 7 0.14
16 7 0.14
17 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:367087 original size:17 final size:17
Alignment explanation
Indices: 367065--367140 Score: 98
Period size: 17 Copynumber: 4.2 Consensus size: 17
367055 TTTGAGTTGA
*
367065 TATTATTATATTATTAC
1 TATTATTATATTATTAT
367082 TATTATTATATATAATTAT
1 TATTATTATAT-T-ATTAT
367101 ATATATATTATATTATTAT
1 -TAT-TATTATATTATTAT
*
367120 TATTACTATATTATTAT
1 TATTATTATATTATTAT
367137 TATT
1 TATT
367141 TACAAGACCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
17 28 0.53
18 4 0.08
19 9 0.17
20 4 0.08
21 8 0.15
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATTATATTATTAT
Found at i:367101 original size:10 final size:11
Alignment explanation
Indices: 367071--367133 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
367061 TTGATATTAT
367071 TATATTAT-TA
1 TATATTATATA
367081 CTATTATTATATA
1 -TA-TATTATATA
367094 TA-ATTATATA
1 TATATTATATA
367104 TATATTATAT-
1 TATATTATATA
367114 TATTATTAT-TA
1 TA-TATTATATA
367125 CTATATTAT
1 -TATATTAT
367134 TATTATTTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
10 13 0.28
11 21 0.46
12 10 0.22
13 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATTATATA
Found at i:371476 original size:14 final size:14
Alignment explanation
Indices: 371457--371486 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
371447 ATAAAATCAT
371457 TCATATGCCATATC
1 TCATATGCCATATC
371471 TCATATGCCATATC
1 TCATATGCCATATC
371485 TC
1 TC
371487 TAGCACACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.37
Consensus pattern (14 bp):
TCATATGCCATATC
Found at i:371767 original size:699 final size:695
Alignment explanation
Indices: 370376--371774 Score: 1824
Period size: 699 Copynumber: 2.0 Consensus size: 695
370366 TTACCTCATT
* * ** * * *
370376 AAAAGTATCTTGATAGAAGAGGCATTGAATTGCTTCGTTACGGTCCATATTACAATCTCTAAAGA
1 AAAAGTATCTTCATAGAAGAGGCAATGAACGGCGTCGTTACGCTCCATATTACAATCTATAAAGA
* *
370441 CGACAAAGATCTCTCAGTCCATGCAACTATTACTAACAATCTCTTTAAGATTCATTAAAGACTAT
66 CGACAAAGATCTCTCAATACATGCAACTATTACTAACAATCTCTTTAAGATTCATTAAAGACTAT
** * * *
370506 AATATAGACCCTAGCGATTCCGTTCAATGTTTCCTCTCCCAGGATACTTTTCAAGAGGTAAAAAG
131 AATATAGACCCTAGCGACACCGTTCAATGCTTCCTCTCCCAAGATAATTTTCAAGAGGTAAAAAG
* *
370571 CAAACAAGAAATACTCAAAGAAGAAAAGAGATGAAAAGGAAAGGAACTAATGTATTTTTTTATTG
196 CAAACAAGAAAGACTC---------AAGAGATGAAAAGAAAAGGAACTAATGTATTTTTTTATTG
*
370636 AACAACTTACTTTAATGAATTACAAACAAACTTGGGTATTTTATAGCCCAAATATAATTACCCAA
252 AACAACTAACTTTAATGAATTACAAACAAACTTGGGTATTTTATAGCCCAAATATAATTACCCAA
* * * * *
370701 AACATAAATAATTTGAGATGCATTTTAACTTGAATGTGATTGATTAAAACATAAACGACGTTCAT
317 AACATAAATAATTAGAGATGAATTTTAACTTAAATGTGACTGATTAAAACATAAAC-ACATTCAT
* ** *
370766 CAAATCTCATATGCCACATCTTTAGCATTCCAACTTTCATCTTTCTAATTTAGCTTTCATACTTT
381 CAAATCTCATATGCCACATCTCTAGCACACCAACTTTCATCTTTCTAATTTAGCTTTCAAACTTT
* ** ** *
370831 TTTAAGCATATTTTAAACATTATTTAAATTTAGAATCATTACATATTTGATTCAAATTAGTGTCT
446 TTT-AGCATATTTTAAACATTATTCAAATTTAGAATCAGAACATATTCAATTCAAACTAGTGTCT
* *
370896 TTTTACCATATTCAATTTCATAATTTAATCCTTCAAAAATTATTTTCTGATCATCAAATGTCAAA
510 TTTTACAATATTCAATTTCATAATTTAATCCTTCAAAAATTATTTTCTGATCATCAAACGTCAAA
* * **
370961 AAAATTCATAAACAAAATTCTGAGTGTTAAAAAAAGATCATCTTACATCAATTAGGATTCCCTCT
575 AAAATTCATAAACAAAATTCGGAGTGTTAAAAAAAGACCATCTTACATCAACGAGGATTCCCTCT
* * *
371026 CATATGGATATAAATGAAAAGACAAAAACAACCTAATTGATATGAACATTCTTATG
640 CATAAGGATATAAAAGAAAAGACAAAAACAACATAATTGATATGAACATTCTTATG
* *
371082 AAAAGTATCTTCATA-AAGGAGGCAATGAACGGCGTCGTTACGCTTCATATTACAATCTATAAGG
1 AAAAGTATCTTCATAGAA-GAGGCAATGAACGGCGTCGTTACGCTCCATATTACAATCTATAAAG
* * * ** * *
371146 ATGGCGAAGATCTCTCAATATGTGCAACTATTATTAACAATCTCTTTAAGATTCATTAAAGACTG
65 ACGACAAAGATCTCTCAATACATGCAACTATTACTAACAATCTCTTTAAGATTCATTAAAGACTA
* * *
371211 TAATATGGACCCTAGCGACACTGTTCAATGCTTCCTCTCTCAAGATAATTTTCAAGAGGTAAAAA
130 TAATATAGACCCTAGCGACACCGTTCAATGCTTCCTCTCCCAAGATAATTTTCAAGAGGT-AAAA
* ** * *
371276 AGTAAACGGGAAAGACTC-AGCGATGAAAAGAAAAGGAACTAATGTA-TTTTTTATTGAACTACT
194 AGCAAACAAGAAAGACTCAAGAGATGAAAAGAAAAGGAACTAATGTATTTTTTTATTGAACAACT
* * *
371339 AACTTTAATGAATTACAAACAACCTTGGGTATTTTATAGCTCAAATATAATTACCCAAACCATAA
259 AACTTTAATGAATTACAAACAAACTTGGGTATTTTATAGCCCAAATATAATTACCCAAAACATAA
371404 ATAATTAGAGAT-AATTTTTAACTTAAATGTGACTGATTAAAACATAAA-ATCATTCATATGCCA
324 ATAATTAGAGATGAA-TTTTAACTTAAATGTGACTGATTAAAACATAAACA-CATTC--AT--CA
* * *
371467 TATCTCATATGCCATATCTCTAGCACACCAACTTTCATCTTTCTAATTTAGTTTTCAAACTATTT
383 AATCTCATATGCCACATCTCTAGCACACCAACTTTCATCTTTCTAATTTAGCTTTCAAACT-TTT
* * * *
371532 TT-GCCATATTTTAAACCTTATTCAAATTTCGAATTAGAACATATTCAATTCAAACTAGTTTCTT
447 TTAG-CATATTTTAAACATTATTCAAATTTAGAATCAGAACATATTCAATTCAAACTAGTGTCTT
* * * * *
371596 TTTACAATATTC-ATTTTATAATTTACTCCTTCAAAAATTATTTTCTGATCATCAGACGTTAGAA
511 TTTACAATATTCAATTTCATAATTTAATCCTTCAAAAATTATTTTCTGATCATCAAACGTCAAAA
** * *
371660 AAATTC-TAAACCAAGTTTCGGAGTGTTAAAAAAAAGACCATTTTACATCAACGATGATTCCCTC
576 AAATTCATAAA-CAAAATTCGGAGTGTT-AAAAAAAGACCATCTTACATCAACGAGGATTCCCTC
* *
371724 TTATAAGGATATAAAAGAAAAGACAAAAACAACATATTTGATATGAACATT
639 TCATAAGGATATAAAAGAAAAGACAAAAACAACATAATTGATATGAACATT
371775 GTAGAAACTC
Statistics
Matches: 602, Mismatches: 79, Indels: 31
0.85 0.11 0.04
Matches are distributed among these distances:
694 1 0.00
695 5 0.01
696 119 0.20
697 32 0.05
698 66 0.11
699 194 0.32
700 5 0.01
705 2 0.00
706 160 0.27
707 18 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (695 bp):
AAAAGTATCTTCATAGAAGAGGCAATGAACGGCGTCGTTACGCTCCATATTACAATCTATAAAGA
CGACAAAGATCTCTCAATACATGCAACTATTACTAACAATCTCTTTAAGATTCATTAAAGACTAT
AATATAGACCCTAGCGACACCGTTCAATGCTTCCTCTCCCAAGATAATTTTCAAGAGGTAAAAAG
CAAACAAGAAAGACTCAAGAGATGAAAAGAAAAGGAACTAATGTATTTTTTTATTGAACAACTAA
CTTTAATGAATTACAAACAAACTTGGGTATTTTATAGCCCAAATATAATTACCCAAAACATAAAT
AATTAGAGATGAATTTTAACTTAAATGTGACTGATTAAAACATAAACACATTCATCAAATCTCAT
ATGCCACATCTCTAGCACACCAACTTTCATCTTTCTAATTTAGCTTTCAAACTTTTTTAGCATAT
TTTAAACATTATTCAAATTTAGAATCAGAACATATTCAATTCAAACTAGTGTCTTTTTACAATAT
TCAATTTCATAATTTAATCCTTCAAAAATTATTTTCTGATCATCAAACGTCAAAAAAATTCATAA
ACAAAATTCGGAGTGTTAAAAAAAGACCATCTTACATCAACGAGGATTCCCTCTCATAAGGATAT
AAAAGAAAAGACAAAAACAACATAATTGATATGAACATTCTTATG
Found at i:375319 original size:25 final size:23
Alignment explanation
Indices: 375285--375338 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
375275 AAATCATCAA
*
375285 TTTTTCAAAATAAAAATCATAATTG
1 TTTTTTAAAAT-AAAAT-ATAATTG
* *
375310 TTTTTTAAAATAATATTTAATTG
1 TTTTTTAAAATAAAATATAATTG
375333 TTTTTT
1 TTTTTT
375339 TTACAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
24 4 0.15
25 10 0.38
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTTTAAAATAAAATATAATTG
Found at i:380300 original size:37 final size:36
Alignment explanation
Indices: 380250--380390 Score: 144
Period size: 37 Copynumber: 3.9 Consensus size: 36
380240 CAGCATCATG
*
380250 AAACAAATTTTGTCTTGCTTGAGACAATTTTTATTAA
1 AAACAAATTTTGTCTTGCTTGAGACAATTTTT-CTAA
* * *
380287 AAACAAATTTTGTCTCGCTTGAGAGAGTTTTCTCTAA
1 AAACAAATTTTGTCTTGCTTGAGACAATTTT-TCTAA
* * * *
380324 AAATAAATTTTTTCTTGCTGGAGACAATTTTTCT-G
1 AAACAAATTTTGTCTTGCTTGAGACAATTTTTCTAA
* *
380359 AAAC-AATTTTCATCTCGCTTGAGAC-ATTTTTC
1 AAACAAATTTT-GTCTTGCTTGAGACAATTTTTC
380391 CTTTGAGATG
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
34 13 0.15
35 14 0.16
36 3 0.03
37 56 0.64
38 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (36 bp):
AAACAAATTTTGTCTTGCTTGAGACAATTTTTCTAA
Found at i:380768 original size:29 final size:30
Alignment explanation
Indices: 380725--380791 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
380715 AGACAATTTT
* * *
380725 CCTTAAAACACCAAA-TTTGGAAATTGTTTC
1 CCTTGAAACACCAAACATT-GAAATCGTTTC
*
380755 CCTTGAAACA-CAAACATTGAGATCGTTTC
1 CCTTGAAACACCAAACATTGAAATCGTTTC
380784 CCTTGAAA
1 CCTTGAAA
380792 TGAATTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (30 bp):
CCTTGAAACACCAAACATTGAAATCGTTTC
Found at i:380819 original size:36 final size:35
Alignment explanation
Indices: 380771--380864 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 35
380761 AACACAAACA
* *
380771 TTGAGATC-GTTTCCCTTGAAATGAATTTTGTCTCTC
1 TTGAGA-CAGTTTCTCTTGAAA-AAATTTTGTCTCTC
380807 TTGAGACAGTTTCTCTTGTAACAAAATTTTGTCTCTC
1 TTGAGACAGTTTCTCTTG-AA-AAAATTTTGTCTCTC
*
380844 TTGAAACAGTTTCTCTTGAAA
1 TTGAGACAGTTTCTCTTGAAA
380865 CATCATCTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.04
36 17 0.33
37 32 0.62
38 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (35 bp):
TTGAGACAGTTTCTCTTGAAAAAATTTTGTCTCTC
Found at i:380841 original size:37 final size:37
Alignment explanation
Indices: 380794--380866 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
380784 CCTTGAAATG
* *
380794 AATTTTGTCTCTCTTGAGACAGTTTCTCTTGTAACAA
1 AATTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAA
380831 AATTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACA
380867 TCATCTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAA
Found at i:381182 original size:130 final size:132
Alignment explanation
Indices: 380938--381288 Score: 336
Period size: 130 Copynumber: 2.7 Consensus size: 132
380928 AACAAAACCC
* * * * * ** * * *
380938 TAAAGATGGCCAGCCGTCCTCATCGCATAGGAACCGCGTCATCCACCGACCAAGCCTCCTCATCA
1 TAAAGATGGCCAGTCATCCTCATCACGTAAGAACCATGCCATCCACTGACCAAACCTCCTCATCA
** * * * * *
381003 CGTAGGAGCAATGTCACCCTTATATAACCAGTCGTCCTCATCACTTAGGAAC-CACATTATCATC
66 CGTAGGAGCTGTGTCACCCTTAGATAACCACTCGTCCTAATCACGTAGGAACTCACATCATCATC
381067 CA
131 CA
381069 TAAAGATGG-CA-TACCATCCTCATCACGTAAGAACCATGCCAT-CACTGACCAAACCTCCTCAT
1 TAAAGATGGCCAGT--CATCCTCATCACGTAAGAACCATGCCATCCACTGACCAAACCTCCTCAT
* * * ***
381131 CACATAGGAGCTGTATCACCCTTAGATAACCAACT-GTCCTAATCGCGTAGGAACTGTGTTATCA
64 CACGTAGGAGCTGTGTCACCCTTAGATAACC-ACTCGTCCTAATCACGTAGGAAC--TCACATCA
*
381195 TCATCCC
126 TCATCCA
* * * * *
381202 TAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGATCTCCTCATCA
1 TAAAGATGGCCAGTCATCCTCATCACGTAAGAACCATGCCATCCACTGACCAAACCTCCTCATCA
*
381267 TGTAGGAG-TCGTGTCACCCTTA
66 CGTAGGAGCT-GTGTCACCCTTA
381289 AACGACTAGA
Statistics
Matches: 178, Mismatches: 32, Indels: 17
0.78 0.14 0.07
Matches are distributed among these distances:
130 62 0.35
131 32 0.18
133 44 0.25
134 39 0.22
135 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.23
Consensus pattern (132 bp):
TAAAGATGGCCAGTCATCCTCATCACGTAAGAACCATGCCATCCACTGACCAAACCTCCTCATCA
CGTAGGAGCTGTGTCACCCTTAGATAACCACTCGTCCTAATCACGTAGGAACTCACATCATCATC
CA
Found at i:381483 original size:3 final size:3
Alignment explanation
Indices: 381475--381516 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
381465 GTCTTAAAAA
* * *
381475 TAT TAT TAT TAT TGT TAT TAT TAT TAT TTT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
381517 CATCAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:381495 original size:15 final size:15
Alignment explanation
Indices: 381475--381516 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
381465 GTCTTAAAAA
381475 TATTATTATTATTGT
1 TATTATTATTATTGT
*
381490 TATTATTATTATTTT
1 TATTATTATTATTGT
*
381505 TAATATTATTAT
1 TATTATTATTAT
381517 CATCAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTATTGT
Found at i:382711 original size:31 final size:32
Alignment explanation
Indices: 382655--382717 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
382645 CTGCCTTACA
* *
382655 TATGGTTTAATTATCATTTACTCCTTATTGTT
1 TATGGTTTAATTATAATTTACTCCTTAATGTT
* *
382687 TATGGTTTAGTT-TAATTTAGTCCTTAATGTT
1 TATGGTTTAATTATAATTTACTCCTTAATGTT
382718 ATTTAGGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.56
Consensus pattern (32 bp):
TATGGTTTAATTATAATTTACTCCTTAATGTT
Found at i:383755 original size:24 final size:26
Alignment explanation
Indices: 383709--383762 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
383699 AAATCGTCAA
383709 TTTTTGAAAATAAAAGTTGTAATTGT
1 TTTTTGAAAATAAAAGTTGTAATTGT
* *
383735 TTTTTTAAAATAATA-TT-TAATTGT
1 TTTTTGAAAATAAAAGTTGTAATTGT
383759 TTTT
1 TTTT
383763 ACAAAAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 11 0.42
25 2 0.08
26 13 0.50
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (26 bp):
TTTTTGAAAATAAAAGTTGTAATTGT
Found at i:388023 original size:13 final size:13
Alignment explanation
Indices: 387991--388015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
387981 TTATTGACAA
387991 ATTTTCTTTTATC
1 ATTTTCTTTTATC
388004 ATTTTCTTTTAT
1 ATTTTCTTTTAT
388016 TTTATTCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTCTTTTATC
Found at i:390626 original size:14 final size:14
Alignment explanation
Indices: 390607--390633 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
390597 TCGCCTAGGA
390607 TTTGAACCATGGGC
1 TTTGAACCATGGGC
390621 TTTGAACCATGGG
1 TTTGAACCATGGG
390634 TTGATCGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (14 bp):
TTTGAACCATGGGC
Found at i:392145 original size:18 final size:18
Alignment explanation
Indices: 392122--392164 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
392112 AAATTTTACA
392122 AAGAAGCTGCTAAAGAAG
1 AAGAAGCTGCTAAAGAAG
*
392140 AAGAAGCTGTTAAAGAAG
1 AAGAAGCTGCTAAAGAAG
392158 AAGAAGC
1 AAGAAGC
392165 AGAGATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.28, T:0.12
Consensus pattern (18 bp):
AAGAAGCTGCTAAAGAAG
Done.