Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_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: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:280943 original size:42 final size:43
Alignment explanation
Indices: 280853--280955 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 43
280843 TATATATCTA
* * * *
280853 GACCTTTTGCGACGTTTGTTCCAAAAACACCGATGTATATATT
1 GACCTTTTACGATGTTTGTTCCAAAAACACCGATGTAGATATC
* * *
280896 GACCTTTTACGGTGTTTGTTCC-AAAACGCCGCTGTAGATATC
1 GACCTTTTACGATGTTTGTTCCAAAAACACCGATGTAGATATC
280938 GACCTTTTACGATGTTTG
1 GACCTTTTACGATGTTTG
280956 GCTATAGTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 33 0.63
43 19 0.37
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (43 bp):
GACCTTTTACGATGTTTGTTCCAAAAACACCGATGTAGATATC
Found at i:281135 original size:2 final size:2
Alignment explanation
Indices: 281128--281160 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
281118 AATACTTAAC
281128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
281161 TTAACTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:285571 original size:33 final size:33
Alignment explanation
Indices: 285534--285605 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
285524 TTGGCAAGTT
* *
285534 GGAAATTTTATCTTGGTTGGTGGCCAACTTATG
1 GGAAAATTCATCTTGGTTGGTGGCCAACTTATG
*
285567 GGAAAATTCATCTTGGTTGGTGGCCAACTTATT
1 GGAAAATTCATCTTGGTTGGTGGCCAACTTATG
285600 GGAAAA
1 GGAAAA
285606 ACCTTTGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (33 bp):
GGAAAATTCATCTTGGTTGGTGGCCAACTTATG
Found at i:291517 original size:14 final size:14
Alignment explanation
Indices: 291498--291534 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
291488 CATTTTTATT
291498 TAATTTTATATTTA
1 TAATTTTATATTTA
291512 TAATTTTATATTTA
1 TAATTTTATATTTA
291526 TAATTTTAT
1 TAATTTTAT
291535 CTTGATCACG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TAATTTTATATTTA
Found at i:301956 original size:19 final size:17
Alignment explanation
Indices: 301932--301967 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
301922 TTTTTCTAAA
301932 ATTTTGTTTTCATTTTTTT
1 ATTTTG-TTT-ATTTTTTT
301951 ATTTTGTTTATTTTTTT
1 ATTTTGTTTATTTTTTT
301968 TTCAAATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (17 bp):
ATTTTGTTTATTTTTTT
Found at i:303861 original size:2 final size:2
Alignment explanation
Indices: 303854--303879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
303844 ATATAACATA
303854 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
303880 CAATTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304858 original size:47 final size:47
Alignment explanation
Indices: 304793--304886 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
304783 CAATGATTCC
304793 CAACTTATCAACAAGCCTCCTTACTTCAATGGAGCCAACTATGCCAA
1 CAACTTATCAACAAGCCTCCTTACTTCAATGGAGCCAACTATGCCAA
*
304840 CAACTTATCAATAAGCCTCCTTACTTCAATGGAGCCAACTATGCCAA
1 CAACTTATCAACAAGCCTCCTTACTTCAATGGAGCCAACTATGCCAA
304887 TTGGAAGAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.24
Consensus pattern (47 bp):
CAACTTATCAACAAGCCTCCTTACTTCAATGGAGCCAACTATGCCAA
Found at i:311825 original size:22 final size:18
Alignment explanation
Indices: 311778--311822 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
311768 TTAATGCATC
311778 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
311796 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
311814 TAGTTCATT
1 TAGTTCATT
311823 CATCAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.42
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:313402 original size:32 final size:32
Alignment explanation
Indices: 313366--313436 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
313356 GATGGTCAAT
313366 CTGAGAGAATAATAAAAGTACTCAAAGACATG
1 CTGAGAGAATAATAAAAGTACTCAAAGACATG
313398 CTGAGAGAATAATAAAAGTACTCAAAGACATG
1 CTGAGAGAATAATAAAAGTACTCAAAGACATG
*
313430 CTTAGAG
1 CTGAGAG
313437 CTTGTGTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.20
Consensus pattern (32 bp):
CTGAGAGAATAATAAAAGTACTCAAAGACATG
Found at i:316867 original size:27 final size:27
Alignment explanation
Indices: 316829--316885 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
316819 TGGTGAACTA
316829 TTTCACCTAAGACCCTTACCGATTTGT
1 TTTCACCTAAGACCCTTACCGATTTGT
316856 TTTCACCTAAGACCCTTACCGATTTGT
1 TTTCACCTAAGACCCTTACCGATTTGT
316883 TTT
1 TTT
316886 AGCTCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (27 bp):
TTTCACCTAAGACCCTTACCGATTTGT
Found at i:317597 original size:68 final size:68
Alignment explanation
Indices: 317487--317624 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 68
317477 TTTCAATCTT
* * *
317487 TTCGATTAAGTCCTTATCTAATTCAACTAATTTAAATTTCAATTCAACTTGGTTTTTATCTTAGG
1 TTCGATTAAGTCCTTATATAATTCAACTAATTTAAATCTCAATTCAACTTGGTTTTTATCCTAGG
317552 CAA
66 CAA
** * *
317555 TTCGATTGGGTCCTTATATAATTCAATTAATTTAAATCTCAATTCAATTTGGTTTTTATCCTAGG
1 TTCGATTAAGTCCTTATATAATTCAACTAATTTAAATCTCAATTCAACTTGGTTTTTATCCTAGG
317620 CAA
66 CAA
317623 TT
1 TT
317625 TACCTTAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (68 bp):
TTCGATTAAGTCCTTATATAATTCAACTAATTTAAATCTCAATTCAACTTGGTTTTTATCCTAGG
CAA
Found at i:319710 original size:66 final size:66
Alignment explanation
Indices: 319635--319769 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
319625 AATATATTTA
319635 TTAGATAGTTAATTAAATGTAATATAAAAATAATTTAAAGATAAATTTATTTAGTTTTGTTTGTT
1 TTAGATAGTTAATTAAATGTAATATAAAAATAATTTAAAGATAAATTTATTTAGTTTTGTTTGTT
319700 C
66 C
319701 TTAGATAGTTAATTAAATGTAATATAAAAATAATTTAAAGATAAATTTATTTAGTTTTGTTTGTT
1 TTAGATAGTTAATTAAATGTAATATAAAAATAATTTAAAGATAAATTTATTTAGTTTTGTTTGTT
319766 C
66 C
319767 TTA
1 TTA
319770 CAATTCAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.47
Consensus pattern (66 bp):
TTAGATAGTTAATTAAATGTAATATAAAAATAATTTAAAGATAAATTTATTTAGTTTTGTTTGTT
C
Found at i:322684 original size:24 final size:24
Alignment explanation
Indices: 322630--322702 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
322620 CGTTCGTGAA
* *
322630 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTC
* *
322656 TGTTCATTTATATTCATTTATGTC
1 CGTTCATTTATGTTCATTTATGTC
322680 CGTTCATTTATGTTCATTTATGT
1 CGTTCATTTATGTTCATTTATGT
322703 TCGAACAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 34 0.83
25 3 0.07
26 4 0.10
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.56
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTC
Found at i:322694 original size:10 final size:10
Alignment explanation
Indices: 322656--322704 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
322646 CGTTTATGTT
322656 TGTTCATTTA
1 TGTTCATTTA
*
322666 TATTCATTTA
1 TGTTCATTTA
322676 TGTCCGTTCATTTA
1 --T--GTTCATTTA
322690 TGTTCATTTA
1 TGTTCATTTA
322700 TGTTC
1 TGTTC
322705 GAACAGAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 23 0.70
12 2 0.06
14 8 0.24
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.57
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:323031 original size:20 final size:20
Alignment explanation
Indices: 323006--323045 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
322996 CGTTTATGTT
*
323006 CGTTCGTTTGTGGTTGTTTA
1 CGTTCGTTTATGGTTGTTTA
*
323026 CGTTCGTTTATGTTTGTTTA
1 CGTTCGTTTATGGTTGTTTA
323046 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.25, T:0.57
Consensus pattern (20 bp):
CGTTCGTTTATGGTTGTTTA
Found at i:326010 original size:108 final size:109
Alignment explanation
Indices: 325860--326242 Score: 340
Period size: 108 Copynumber: 3.4 Consensus size: 109
325850 TTTTTAAAGC
* * * *
325860 TGATGGGGCCTTAGAAATCCGACGATCACAAAATGGGTTAATTGCTTGATTTGTTATCAA-TATT
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGATTTGTTATCAACTATT
325924 ATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAAT
66 ATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAAT
* * * * **** * *
325968 TGATGGAGCCTTAGAAATCTGACGATAACAAAATAAGATAATTACTGGAAACATTATCAACCATA
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGATTTGTTATCAACTATT
* * * * ** * * *
326033 AT-AATATAATAAGAAGCGCTTATTTAATATAATAGGTAGCACATGTTTAAAGT
66 ATCAACATATTAGGTA--GC--ACCT-A-A-AAT-GTTACCA-AAGTTTAAA-T
* * * * *
326086 TGATGGGGTCTTAGAAATCTGACAATAACAAAATAGGTTAATTACTTGATTTGTTAT-AAGTATT
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGATTTGTTATCAACTATT
* **
326150 ATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGC
66 ATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAAT
* * **
326194 TGACGGAGCCTTAAAAATCCGACGATAACAAAATTTGTTAATTACTTGA
1 TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGA
326243 CACATTATCG
Statistics
Matches: 207, Mismatches: 56, Indels: 24
0.72 0.20 0.08
Matches are distributed among these distances:
108 98 0.47
109 11 0.05
110 7 0.03
111 3 0.01
112 3 0.01
113 2 0.01
114 2 0.01
115 3 0.01
116 7 0.03
117 14 0.07
118 57 0.28
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (109 bp):
TGATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGATTTGTTATCAACTATT
ATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAAT
Found at i:326102 original size:226 final size:225
Alignment explanation
Indices: 325781--326387 Score: 824
Period size: 226 Copynumber: 2.7 Consensus size: 225
325771 CATAACCAGT
* *
325781 TAATTACTCGAAACATTATCAACCATAATAATAT-AT-AGATAGCGTTTATGTAACGTAATAGGT
1 TAATTACTCGAAACATTATCAACCATAATAATATAATAAGA-AGCGTTTATTTAATGTAATAGGT
* * * * *
325844 AGCCTCTTTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATCACAAAATGGGTTAATTGCTTGA
65 AGCC-ATGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGA
* *
325909 TTTGTTATCAATATTATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAATTGATGG
129 TTTGTTATCAATATTATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAACTGACGG
* *
325974 AGCCTTAGAAATCTGACGATAACAAAATAAGA
194 AGCCTTAAAAATCCGACGATAACAAAATAAGA
* * *
326006 TAATTACTGGAAACATTATCAACCATAATAATATAATAAGAAGCGCTTATTTAATATAATAGGTA
1 TAATTACTCGAAACATTATCAACCATAATAATATAATAAGAAGCGTTTATTTAATGTAATAGGTA
* * * *
326071 GCACATGTTTAAAGTTGATGGGGTCTTAGAAATCTGACAATAACAAAATAGGTTAATTACTTGAT
66 GC-CATGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAT
* *
326136 TTGTTAT-AAGTATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGACGG
130 TTGTTATCAA-TATTATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAACTGACGG
** *
326200 AGCCTTAAAAATCCGACGATAACAAAATTTGT
194 AGCCTTAAAAATCCGACGATAACAAAATAAGA
* * * * * * * *
326232 TAATTACTTGACACATTATCGACTATAATAACATAACAAGTAGCGTTTATTTAATGTAATAGCTA
1 TAATTACTCGAAACATTATCAACCATAATAATATAATAAGAAGCGTTTATTTAATGTAATAGGTA
* * * *
326297 GCGCTTGTTTAAAGCTGATGGGGCCTTAGAAATCCAACGATAACAAAATATGTTAATTAATTGAT
66 GC-CATGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAT
*
326362 TTGTTATCAGTATTATCAACATATTA
130 TTGTTATCAATATTATCAACATATTA
326388 TCGTGTAAAT
Statistics
Matches: 334, Mismatches: 43, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
225 35 0.10
226 294 0.88
227 5 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (225 bp):
TAATTACTCGAAACATTATCAACCATAATAATATAATAAGAAGCGTTTATTTAATGTAATAGGTA
GCCATGTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGATT
TGTTATCAATATTATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAACTGACGGAG
CCTTAAAAATCCGACGATAACAAAATAAGA
Found at i:327017 original size:177 final size:178
Alignment explanation
Indices: 326716--327060 Score: 461
Period size: 177 Copynumber: 1.9 Consensus size: 178
326706 TTATATATGT
* *
326716 GTATCGATACATTTTGCGTGCAAATTGTTTGAGATACATACTGAACTAAAAGTATTGATACCTAT
1 GTATCGATACATTTTGAGTGCAAATTGTTTGAGATACATACTGAACTAAAAGTATCGATACCTAT
* * *
326781 ATATAAAGTATCGATACTTGGTATATACGCCTTTGATCATTATACCGGTAAACTTTTACCCTTTA
66 ATAAAAAGTATCGATAC-TGGTATATACGCCTTTGATCATTAAACCAGTAAACTTTTACCCTTTA
*
326846 CATTGTTAATTTACCTATTACTTT-ATAGTAATAGGTTTTGGAATTAAAA
130 CATTGTAAATTTACCTATTACTTTGA-AGTAATAGGTTTTGGAATTAAAA
* *
326895 GTATCGATAC-TTTTTAGTGCAAATTGTTTGAGA-AGCATACTAGAA-TAAAAGTATCGATGCCT
1 GTATCGATACATTTTGAGTGCAAATTGTTTGAGATA-CATACT-GAACTAAAAGTATCGATACCT
* * * * *
326957 ATA-AAAAAGTATCGATA-TGTTATATTTACGCCTATT-TTCATTAAACCAGTAGATTTTTACCT
64 ATATAAAAAGTATCGATACTGGTATA--TACGCCT-TTGATCATTAAACCAGTAAACTTTTACCC
327019 TTTACATTGTAAATTTACCTATTACTTTGAAGTAATAGGTTT
126 TTTACATTGTAAATTTACCTATTACTTTGAAGTAATAGGTTT
327061 CGAAATTCTG
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
175 6 0.04
177 80 0.54
178 48 0.33
179 13 0.09
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (178 bp):
GTATCGATACATTTTGAGTGCAAATTGTTTGAGATACATACTGAACTAAAAGTATCGATACCTAT
ATAAAAAGTATCGATACTGGTATATACGCCTTTGATCATTAAACCAGTAAACTTTTACCCTTTAC
ATTGTAAATTTACCTATTACTTTGAAGTAATAGGTTTTGGAATTAAAA
Found at i:330859 original size:23 final size:23
Alignment explanation
Indices: 330806--330859 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
330796 TCGATTACCC
*
330806 TAAGAGGGGAATCAGTTCCCCTT
1 TAAGGGGGGAATCAGTTCCCCTT
* * ** *
330829 CAAAGGGGGAATTGGTTCCTCTT
1 TAAGGGGGGAATCAGTTCCCCTT
330852 TAAGGGGG
1 TAAGGGGG
330860 TATAGATTCC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (23 bp):
TAAGGGGGGAATCAGTTCCCCTT
Found at i:336911 original size:8 final size:8
Alignment explanation
Indices: 336898--336926 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
336888 ATATACTTAG
336898 AAAATCTT
1 AAAATCTT
336906 AAAATCTT
1 AAAATCTT
336914 AAAATCTT
1 AAAATCTT
336922 AAAAT
1 AAAAT
336927 TCATTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATCTT
Found at i:338494 original size:10 final size:10
Alignment explanation
Indices: 338479--338503 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
338469 AAAGATAAAA
338479 TAAAACAAAT
1 TAAAACAAAT
338489 TAAAACAAAT
1 TAAAACAAAT
338499 TAAAA
1 TAAAA
338504 GTTAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (10 bp):
TAAAACAAAT
Found at i:338913 original size:30 final size:30
Alignment explanation
Indices: 338843--339012 Score: 101
Period size: 30 Copynumber: 5.7 Consensus size: 30
338833 AACAAAATTG
* * *
338843 AAAACTTAAAAGATTAAAATAATAAAAACA
1 AAAAGTTAAAGGACTAAAATAATAAAAACA
*
338873 AAAAGTTAAAGGACTAAAATAGA-AAAAATA
1 AAAAGTTAAAGGACTAAAATA-ATAAAAACA
* ** ** *
338903 AAAAGTTAAAGG-GTTGAACCATAAATACA
1 AAAAGTTAAAGGACTAAAATAATAAAAACA
* * * * * * * *
338932 GAAAGATAAAGGACCACAATAGTTAATATA
1 AAAAGTTAAAGGACTAAAATAATAAAAACA
* * *
338962 GAAATTTAAAGGACTAAAATAATAAAAATA
1 AAAAGTTAAAGGACTAAAATAATAAAAACA
* * *
338992 GAAACTTAAGGGACTAAAATA
1 AAAAGTTAAAGGACTAAAATA
339013 GCTAAAATAG
Statistics
Matches: 106, Mismatches: 31, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
28 1 0.01
29 18 0.17
30 86 0.81
31 1 0.01
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (30 bp):
AAAAGTTAAAGGACTAAAATAATAAAAACA
Found at i:339020 original size:30 final size:30
Alignment explanation
Indices: 338949--339040 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
338939 AAAGGACCAC
* * * *
338949 AATAGTTAATATAGAAATTTAAAGGACTAA
1 AATAGATAAAATAGAAACTTAAGGGACTAA
338979 AATA-ATAAAAATAGAAACTTAAGGGACTAA
1 AATAGAT-AAAATAGAAACTTAAGGGACTAA
*
339009 AATAGCTAAAATAGAAACTTAAAGGGA-TAA
1 AATAGATAAAATAGAAACTT-AAGGGACTAA
339039 AA
1 AA
339041 AAAATTGAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 1 0.02
30 46 0.85
31 7 0.13
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (30 bp):
AATAGATAAAATAGAAACTTAAGGGACTAA
Found at i:339040 original size:60 final size:60
Alignment explanation
Indices: 338799--339033 Score: 186
Period size: 60 Copynumber: 3.9 Consensus size: 60
338789 ATAAGGGTCT
* * * * * * * * *
338799 AAATAGTAATAACAGAAATTTACAGGACTAAAACA-ACAAAATTGAAAACTTAAAAGATTA
1 AAATAATAAAAACAGAAAGTTAAAGGACTAAAATAGATAAAATAG-AAACTTAAAGGACTA
* * * * * *
338859 AAATAATAAAAACAAAAAGTTAAAGGACTAAAATAGAAAAAATAAAAAGTTAAAGG-GTT
1 AAATAATAAAAACAGAAAGTTAAAGGACTAAAATAGATAAAATAGAAACTTAAAGGACTA
* ** * * * * * * *
338918 GAACCATAAATACAGAAAGATAAAGGACCACAATAGTTAATATAGAAATTTAAAGGACTA
1 AAATAATAAAAACAGAAAGTTAAAGGACTAAAATAGATAAAATAGAAACTTAAAGGACTA
* * * *
338978 AAATAATAAAAATAGAAACTTAAGGGACTAAAATAGCTAAAATAGAAACTTAAAGG
1 AAATAATAAAAACAGAAAGTTAAAGGACTAAAATAGATAAAATAGAAACTTAAAGG
339034 GATAAAAAAA
Statistics
Matches: 132, Mismatches: 41, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
59 44 0.33
60 82 0.62
61 6 0.05
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.20
Consensus pattern (60 bp):
AAATAATAAAAACAGAAAGTTAAAGGACTAAAATAGATAAAATAGAAACTTAAAGGACTA
Found at i:340092 original size:129 final size:129
Alignment explanation
Indices: 339860--340128 Score: 305
Period size: 129 Copynumber: 2.1 Consensus size: 129
339850 CATTTGTGTG
* *
339860 ACAAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTAGAAAAATGCCGCAATAGGTGTTG
1 ACAAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTACAAAAACGCCGCAATAGGTGTTG
* * *
339925 ATATTTAGCGGCGTTTTTCAGACAAACGCCGTAATAGGT-TATGATGTTTAACGACGTTTTTCTC
66 ATATTTAGCGGCATTTTTCACACAAACGCCGCAATAGGTAT-TGATGTTTAACGACGTTTTTCTC
* * * * * *
339989 ACAAACGA-CGCAGTAGGTGTTGATGTTTTGCGGCGTTT-TTCCCATAAACGCCGCAGTAGGTGT
1 ACAAAC-ACCGCAATAGGTGTTGATATTTAGCGGCGTTTGTT-ACAAAAACGCCGCAATAGGTGT
* * * * *
340052 TGATGTTTTGCGGCATTTTTCTCACAAACGCCGCAGTAGGTATTGATGTTTTGA-GACGTTTTTG
64 TGATATTTAGCGGCATTTTTCACACAAACGCCGCAATAGGTATTGATG-TTTAACGACGTTTTT-
340116 CT-
127 CTC
*
340118 AAAAACACCGC
1 ACAAACACCGC
340129 TAAAGGTCTG
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
128 3 0.03
129 106 0.91
130 8 0.07
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (129 bp):
ACAAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTACAAAAACGCCGCAATAGGTGTTG
ATATTTAGCGGCATTTTTCACACAAACGCCGCAATAGGTATTGATGTTTAACGACGTTTTTCTC
Found at i:340099 original size:43 final size:43
Alignment explanation
Indices: 339860--340114 Score: 253
Period size: 43 Copynumber: 5.9 Consensus size: 43
339850 CATTTGTGTG
* * * * **
339860 ACAAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTGTT-AG
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTT-TTCTC
* * * * * **
339903 AAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCTC
* * ** *
339946 ACAAACGCCGTAATAGGT-TATGATGTTTAACGACGTTTTTCTC
1 ACAAACGCCGCAGTAGGTGT-TGATGTTTTGCGGCGTTTTTCTC
* *
339989 ACAAACGACGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCTC
* *
340032 ATAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCATTTTTCTC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCTC
* * *
340075 ACAAACGCCGCAGTAGGTATTGATGTTTTGAGACGTTTTT
1 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTT
340115 GCTAAAAACA
Statistics
Matches: 182, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
42 3 0.02
43 178 0.98
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCTC
Found at i:341144 original size:14 final size:14
Alignment explanation
Indices: 341125--341156 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
341115 CCTCCTCATG
*
341125 AGCTATACAAGGAA
1 AGCTATACAAGCAA
341139 AGCTATACAAGCAA
1 AGCTATACAAGCAA
341153 AGCT
1 AGCT
341157 CTTCGATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (14 bp):
AGCTATACAAGCAA
Found at i:348810 original size:40 final size:41
Alignment explanation
Indices: 348761--348892 Score: 110
Period size: 40 Copynumber: 3.2 Consensus size: 41
348751 GCGTTTGGTG
*
348761 AAAACGCCACTATATATTACACCTATTGCGGCGTTTTTTAT
1 AAAACGCCACTATATATTAAACCTATTGCGGCGTTTTTTAT
* ** * *
348802 AAAA-GCCACTA-ATGTCTAAATTTTTTGCGGTGTTTGCATTTA-
1 AAAACGCCACTATATAT-TAAACCTATTGCGGCGTTT---TTTAT
* * *
348844 AAAATGCCACTATATATTATACCTATTGCGGC-ATTTTTAT
1 AAAACGCCACTATATATTAAACCTATTGCGGCGTTTTTTAT
348884 AAAAACGCC
1 -AAAACGCC
348893 GCTAAAGTAC
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
39 7 0.10
40 21 0.30
41 11 0.16
42 6 0.09
43 21 0.30
44 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (41 bp):
AAAACGCCACTATATATTAAACCTATTGCGGCGTTTTTTAT
Found at i:350455 original size:41 final size:42
Alignment explanation
Indices: 350350--350467 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
350340 TTTTAGGTAT
* * *
350350 AAACCCCGCTAATTTACCACTCTATTACGGCGTTTGTACCAC
1 AAACACCGCTAAATTACCACTCTATTACGGCGTTTGGACCAC
** * *
350392 AAATGCCGCTAAATTACCACTCTATTACGGCGTTTGGGCTA-
1 AAACACCGCTAAATTACCACTCTATTACGGCGTTTGGACCAC
* *
350433 AAACACCGCTAAATGT-CTACTCTATTGCGGCGTTT
1 AAACACCGCTAAAT-TACCACTCTATTACGGCGTTT
350468 TTACTATAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 29 0.45
42 36 0.55
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (42 bp):
AAACACCGCTAAATTACCACTCTATTACGGCGTTTGGACCAC
Found at i:350626 original size:42 final size:38
Alignment explanation
Indices: 350574--350672 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 38
350564 GCCACTATAA
* * *
350574 ACCACCCTATTACGGTGTTTTAGGTATATATGCCGCTAATTT
1 ACCACTCTATTACGGTGTTTTA--TA-A-ACGCCGCTAAATT
*
350616 ACCACTCTATTACGGCG-TTTATAAACGCCGCTAAATT
1 ACCACTCTATTACGGTGTTTTATAAACGCCGCTAAATT
350653 ACCACTCTATTACGGTGTTT
1 ACCACTCTATTACGGTGTTT
350673 GGGCTAACAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
37 27 0.53
38 3 0.06
39 2 0.04
41 4 0.08
42 15 0.29
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (38 bp):
ACCACTCTATTACGGTGTTTTATAAACGCCGCTAAATT
Found at i:350872 original size:42 final size:43
Alignment explanation
Indices: 350820--350923 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 43
350810 GCCACTACAA
* * * *
350820 ACCACACTATTACGACGTTTTA-GGTATAAATGCCGCTAATTT
1 ACCACTCTATTACGGCGTTTTATGGTACAAATGCCGCTAAATT
*
350862 ACCACTCTATTACGGCG-TTTATGGTACAAGTGCCGCTAAATT
1 ACCACTCTATTACGGCGTTTTATGGTACAAATGCCGCTAAATT
*
350904 ACCAGTCTATTACGGCGTTT
1 ACCACTCTATTACGGCGTTT
350924 GGGCTAAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
41 4 0.07
42 48 0.89
43 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (43 bp):
ACCACTCTATTACGGCGTTTTATGGTACAAATGCCGCTAAATT
Found at i:351023 original size:251 final size:246
Alignment explanation
Indices: 350235--351120 Score: 1190
Period size: 246 Copynumber: 3.6 Consensus size: 246
350225 AAAAATGCCA
* * * * * * * * *
350235 CTATTGATTAACACTATTATGGCGTTTGTCAAAAAACGATG-TTAAATTATTTTTCATTACGGCG
1 CTATTGATTAACCCTTTTATGGCGTTTGTCTAAAAACGACGCATAAAGTATTCTTCATTGCGGCA
* * **
350299 TTTGTTGGAAAAACGCCACTATAAACCACCCTATTATGGCATTTTAGGTATAAACCCCGCTAATT
66 TTTGTTGGAAAAACGCCACTATAAACCACCCTATTACGGCGTTTTAGGTATAAATGCCGCTAATT
**
350364 TACCACTCTATTACGGCGTTTGTACCACAAATGCCGCTAAATTACCACTCTATTACGGCGTTTGG
131 TACCACTCTATTACGGCG-TT-TATTAC-AATGCCGCTAAATTACCACTCTATTACGGCGTTTGG
*
350429 GCTAAAACACCGCTAAATGTCTACTCTATTGCGGCGTTTTTACTATAAACGCCG
193 GCTAAACCACCGCTAAATGTCTACTCTATTGCGGCGTTTTTACTATAAACGCCG
* *
350483 CTATTGATTAACCCTTTTATGGCATTTTTCTAAAAACGACGCAATAAAAGTATTCTTCATTGCGG
1 CTATTGATTAACCCTTTTATGGCGTTTGTCTAAAAACGACGC-AT-AAAGTATTCTTCATTGCGG
* * *
350548 CATTTGTTGGAAAAATGCCACTATAAACCACCCTATTACGGTGTTTTAGGTATATATGCCGCTAA
64 CATTTGTTGGAAAAACGCCACTATAAACCACCCTATTACGGCGTTTTAGGTATAAATGCCGCTAA
* *
350613 TTTACCACTCTATTACGGCGTTTA-TA-AACGCCGCTAAATTACCACTCTATTACGGTGTTTGGG
129 TTTACCACTCTATTACGGCGTTTATTACAATGCCGCTAAATTACCACTCTATTACGGCGTTTGGG
350676 CT-AACACACCGCTAAATGTCTACTCTATTGCGGCGTTTTTACTATAAACGCCG
194 CTAAAC-CACCGCTAAATGTCTACTCTATTGCGGCGTTTTTACTATAAACGCCG
* *
350729 CTATTGATTAACCCTTTTGTGGCGTTTGTCTAAAAATGACGCAATGAAAGTATTCTTCATTGCGG
1 CTATTGATTAACCCTTTTATGGCGTTTGTCTAAAAACGACGC-AT-AAAGTATTCTTCATTGCGG
* * * *
350794 CATTTGTTGGAAAAATGCCACTACAAACCACACTATTACGACGTTTTAGGTATAAATGCCGCTAA
64 CATTTGTTGGAAAAACGCCACTATAAACCACCCTATTACGGCGTTTTAGGTATAAATGCCGCTAA
*
350859 TTTACCACTCTATTACGGCGTTTATGGTACAAGTGCCGCTAAATTACCAGTCTATTACGGCGTTT
129 TTTACCACTCTATTACGGCGTTTAT--TACAA-TGCCGCTAAATTACCACTCTATTACGGCGTTT
* * * **
350924 GGGCTAAACCACCACTAAATGTCTATTCTATTACATCGTTTTTACTATAAACGCCG
191 GGGCTAAACCACCGCTAAATGTCTACTCTATTGCGGCGTTTTTACTATAAACGCCG
* * * *
350980 CTATTGATTAACCCTTCTGTGGCGTTTGTCTAAAAACGACGCA-AAAGTGTTCTTCATTGCGGCG
1 CTATTGATTAACCCTTTTATGGCGTTTGTCTAAAAACGACGCATAAAGTATTCTTCATTGCGGCA
* * * * * * **
351044 TTTATTGGAAAAACACCACTATAAACCACCCTATTGCGGTGTTTTTGGTAAAAACACCGCTATAT
66 TTTGTTGGAAAAACGCCACTATAAACCACCCTATTACGGCGTTTTAGGTATAAATGCCGCTA-AT
*
351109 TTA-TACTCTATT
130 TTACCACTCTATT
351121 GCAGTGTTTG
Statistics
Matches: 570, Mismatches: 57, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
245 2 0.00
246 228 0.40
248 113 0.20
249 9 0.02
250 6 0.01
251 209 0.37
252 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (246 bp):
CTATTGATTAACCCTTTTATGGCGTTTGTCTAAAAACGACGCATAAAGTATTCTTCATTGCGGCA
TTTGTTGGAAAAACGCCACTATAAACCACCCTATTACGGCGTTTTAGGTATAAATGCCGCTAATT
TACCACTCTATTACGGCGTTTATTACAATGCCGCTAAATTACCACTCTATTACGGCGTTTGGGCT
AAACCACCGCTAAATGTCTACTCTATTGCGGCGTTTTTACTATAAACGCCG
Found at i:351789 original size:36 final size:36
Alignment explanation
Indices: 351715--351789 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
351705 TTTTTATATT
*
351715 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
351751 TTTAATTTT-TAAAATAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAA-AAATTATATAAATATTAT-CAA
351787 TTT
1 TTT
351790 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:351971 original size:20 final size:20
Alignment explanation
Indices: 351935--351972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
351925 ATCCTATTCC
**
351935 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
351955 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
351973 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:352620 original size:3 final size:3
Alignment explanation
Indices: 352612--352659 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
352602 CAAAAAGATG
* *
352612 TAA TAA TAA TAA CACA TAA TAA AAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
352657 TAA
1 TAA
352660 AAACAAGAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:353149 original size:133 final size:133
Alignment explanation
Indices: 352843--353163 Score: 419
Period size: 134 Copynumber: 2.4 Consensus size: 133
352833 GGGCTAGTTG
** * *
352843 TCTAAGGATGACACGGCTCCTACGTGATGAGGATATTTGGTCGGTGGATGACACGGCTCATACAT
1 TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGG-GGATGACACAGCTCATACAT
* * * * * *
352908 GATGAAGAGTTCTAGCCATCTTTAGGAATGGTGATAACTAGGTTCTTACATGATGAGGACGGTTG
65 GATGAAGAGTTATAGCCATCTTTAGGAAGGGTGATAACTAGGTTCCTACATGATGAAGACAGATG
352973 GTTA
130 GTTA
** * *
352977 TCTTGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACAGCTCATACGT
1 TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGG-ATGACACAGCTCATACAT
* * *
353042 GATGAAGAGTTATGGTCATCTTTAGGAAGGGTGAT-ACTCGGTTCCTACATGATGAAGACAGATG
65 GATGAAGAGTTATAGCCATCTTTAGGAAGGGTGATAACTAGGTTCCTACATGATGAAGACAGATG
353106 GTTA
130 GTTA
* * * *
353110 TCTAAGGTTGACACAGCTCCTATGTGATGTGGAGGTCTGGTCGGGGGATGACAC
1 TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTC-GGGGATGACAC
353164 GGTTCCTACG
Statistics
Matches: 162, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
133 73 0.45
134 89 0.55
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (133 bp):
TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGATGACACAGCTCATACATG
ATGAAGAGTTATAGCCATCTTTAGGAAGGGTGATAACTAGGTTCCTACATGATGAAGACAGATGG
TTA
Found at i:353179 original size:133 final size:134
Alignment explanation
Indices: 352843--353179 Score: 433
Period size: 133 Copynumber: 2.5 Consensus size: 134
352833 GGGCTAGTTG
** * * *
352843 TCTAAGGATGACACGGCTCCTACGTGATGAGGATATTTGGTCGGTGGATGACACGGCTCATACAT
1 TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGT
* * * * * *
352908 GATGAAGAGTTCTAGCCATCTTTAGGAATGGTGATAACTAGGTTCTTACATGATGAGGACGGTTG
66 GATGAAGAGTTATAGCCATCTTTAGGAAGGGTGATAACTAGGTTCCTACATGATGAAGACAGATG
352973 GTTA
131 GTTA
** * * *
352977 TCTTGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACAGCTCATACGT
1 TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGT
* * *
353042 GATGAAGAGTTATGGTCATCTTTAGGAAGGGTGAT-ACTCGGTTCCTACATGATGAAGACAGATG
66 GATGAAGAGTTATAGCCATCTTTAGGAAGGGTGATAACTAGGTTCCTACATGATGAAGACAGATG
353106 GTTA
131 GTTA
* * * * * * *
353110 TCTAAGGTTGACACAGCTCCTATGTGATGTGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGC
1 TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGT
353175 GATGA
66 GATGA
353180 GGACGGCATG
Statistics
Matches: 173, Mismatches: 30, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
133 87 0.50
134 86 0.50
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.27
Consensus pattern (134 bp):
TCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGT
GATGAAGAGTTATAGCCATCTTTAGGAAGGGTGATAACTAGGTTCCTACATGATGAAGACAGATG
GTTA
Found at i:353351 original size:65 final size:66
Alignment explanation
Indices: 353209--353333 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 66
353199 GGGATAATGG
* *
353209 TTTCAAGAGAAACTGACTCAAAGATGATGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAAATTC
1 TTTCAAGGGAAACTGACTCAAAGATGACGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAAATTC
353274 A
66 A
* * *
353275 TTTCAAGGGAAAC-GACTCAAAGATGACGTTT-AAAGGGAAATTGTCTCAAGCGAGACAAA
1 TTTCAAGGGAAACTGACTCAAAGATGACGTTTCAAA-AGAAACTGTCTCAAGAGAGACAAA
353334 TTTTGTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 3 0.06
65 38 0.72
66 12 0.23
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (66 bp):
TTTCAAGGGAAACTGACTCAAAGATGACGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAAATTC
A
Found at i:353735 original size:30 final size:29
Alignment explanation
Indices: 353656--353744 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 29
353646 AGAGAGACAA
*
353656 TTTTTTT-AAAGAAATAGACTCAAAGATGA
1 TTTTTTTAAAAGAAATAGACTCAAAGAT-T
* * *
353685 TTTTGTTAAGAGAAACAGACTCAAAGATT
1 TTTTTTTAAAAGAAATAGACTCAAAGATT
*
353714 TTTTTTTCAAAAGGAATAGACTCAAAGATT
1 TTTTTTT-AAAAGAAATAGACTCAAAGATT
353744 T
1 T
353745 GTTTCAAGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 12 0.24
30 38 0.76
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (29 bp):
TTTTTTTAAAAGAAATAGACTCAAAGATT
Found at i:353903 original size:36 final size:36
Alignment explanation
Indices: 353851--353922 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
353841 TTGTATCTCA
*
353851 GAGAAAAAATGTCTCAAGCGAGACGAAATTTGTTTT
1 GAGAAAAAATGTCTCAAGCGAGACAAAATTTGTTTT
* *
353887 GAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTT
1 GAGAAAAAATGTCTCAAGCGAGACAAAATTTGTTTT
353923 AAAATTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (36 bp):
GAGAAAAAATGTCTCAAGCGAGACAAAATTTGTTTT
Found at i:359360 original size:21 final size:21
Alignment explanation
Indices: 359336--359387 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
359326 TAAAACAACA
*
359336 AAAATAGAAACTTAAATGACT
1 AAAATAGAAACTTAAAGGACT
*
359357 AAAA-ATGAAAGTTAAAGGACT
1 AAAATA-GAAACTTAAAGGACT
359378 AAAATAGAAA
1 AAAATAGAAA
359388 AATAGAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.19
Consensus pattern (21 bp):
AAAATAGAAACTTAAAGGACT
Found at i:359486 original size:30 final size:29
Alignment explanation
Indices: 359452--359529 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
359442 GCAAATACAA
*
359452 AAATTTAAAGGTCTAAAATAACTAAAATAG
1 AAATTTAAAGG-CTAAAATAACTAAAACAG
* *
359482 AAATTTAAGGGACTAAAATAGCTAAAACAG
1 AAATTTAAAGG-CTAAAATAACTAAAACAG
*
359512 AAACTTAAAAGGCTAAAA
1 AAA-TTTAAAGGCTAAAA
359530 CAAATATGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 35 0.85
31 6 0.15
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (29 bp):
AAATTTAAAGGCTAAAATAACTAAAACAG
Found at i:360791 original size:3 final size:3
Alignment explanation
Indices: 360783--360853 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
360773 CAAAAAGATG
360783 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
360831 TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
360854 AAATGAGAAC
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:361561 original size:197 final size:197
Alignment explanation
Indices: 361219--361744 Score: 589
Period size: 200 Copynumber: 2.7 Consensus size: 197
361209 TTCTTTTTTC
* * *
361219 ATTTCTTTTCAATTCCTAAAGTATCGATACTATT-ATACATATACTTATAAAAGTATCGAT----
1 ATTTCTTTTAAATTCCTAAAGTACCGATACT-TTGGTACATATACTTATAAAAGTATCGATACAA
* *
361279 ATCGTCAACATATCCGGTAACGCTTTACCTGTTTTGTCAAATTGAAACCGGTTTTGTCAAATTTC
65 AT-TTCAACAT-TCCGGTAACCCTTTACC-GTTTTGTCAAATTGAAACCGGTTTTGTCAAATTTC
* * * ** *
361344 AACCTGTTATATTGTCATGTATCGATACATGTGTGTAAGGTATCGATACTTTATAGGCGCTAT-T
127 AACCTGTTATATTGTCATGTATCAATACATGTGTGTAACGTATCGATACTTTAGAAACACTATCT
361408 ATTGCA
192 ATTGCA
* *
361414 A-TTCTTTTAAATTCCTAAAGTACCGATACTTTGGTGCATATACTTATAAAAATATCGATACAAA
1 ATTTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
* * * * *
361478 TTTCAACTATTCTGGTATCCCTTTACCGATTTTGTAAAACTGAAACCGGTTTTGTCAAACTTCAA
66 TTTCAAC-ATTCCGGTAACCCTTTACCG-TTTTGTCAAATTGAAACCGGTTTTGTCAAATTTCAA
* * * * *
361543 CCTGTTATATTGTCATGTATTAATACATGTGTGTAACGTATCGATACTTTCGAAACATTTTCCTC
129 CCTGTTATATTGTCATGTATCAATACATGTGTGTAACGTATCGATACTTTAGAAACACTAT-CTA
**
361608 TTTTA
193 TTGCA
* * * ** *
361613 ATTTCTTTTAAATTCCTACATTACTGATACTTTGGTACATATACTTATGCACGTATCGATACAAA
1 ATTTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
* * * * * *
361678 TTTCAACAATTCCGATAGCTCTTTACCGGTTTTCTCAAATTGAAACCGATTTAGTCAAATTTCAA
66 TTTCAAC-ATTCCGGTAACCCTTTACC-GTTTTGTCAAATTGAAACCGGTTTTGTCAAATTTCAA
361743 CC
129 CC
361745 AATTTTGTCT
Statistics
Matches: 276, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
193 2 0.01
194 50 0.18
195 1 0.00
196 1 0.00
197 103 0.37
198 4 0.01
199 5 0.02
200 109 0.39
201 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (197 bp):
ATTTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAA
TTTCAACATTCCGGTAACCCTTTACCGTTTTGTCAAATTGAAACCGGTTTTGTCAAATTTCAACC
TGTTATATTGTCATGTATCAATACATGTGTGTAACGTATCGATACTTTAGAAACACTATCTATTG
CA
Found at i:362817 original size:21 final size:21
Alignment explanation
Indices: 362774--362819 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
362764 TATAATGTTG
* * *
362774 ATTTAACGATAAATTGTAGTT
1 ATTTAACGATAAAATATAATT
*
362795 ATTTAATGATAAAATATAATT
1 ATTTAACGATAAAATATAATT
362816 ATTT
1 ATTT
362820 GGCTGATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (21 bp):
ATTTAACGATAAAATATAATT
Found at i:363898 original size:18 final size:19
Alignment explanation
Indices: 363863--363899 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
363853 CACGGAATGT
363863 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
363883 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
363900 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:368166 original size:380 final size:380
Alignment explanation
Indices: 367465--368221 Score: 1352
Period size: 380 Copynumber: 2.0 Consensus size: 380
367455 AGCAAAGTCG
367465 ACGGCCGTGGAAGGAGGATCAGGATGCCCATCATTTGTGCCGCTCGTGTCTTCCAGTTGACTCGC
1 ACGGCCGTGGAAGGAGGATCAGGATGCCCATCATTTGTGCCGCTCGTGTCTTCCAGTTGACTCGC
* *
367530 GAGTTGGGTCATAAATCCGAATGTCAAACCATTGAGTGGCTCTTTCGTCAGGCCGAACTTTCTAT
66 GAGTTGGGTCATAAATCCGAATGTCAAACCATTGAGTGGCTCTTGCGTCAGGCCGAACCTTCTAT
** *
367595 CATAGCTGCCACTGGCACCGGGACCACCCCCGCCAGCTTCTCCAGCGTCTCGGTTTCCGTTCGCG
131 CATAGCCACCACTGGCACCGGGACCACCCCCGCCAGCTTCTCCACCGTCTCGGTTTCCGTTCGCG
367660 GCGAGGTTAATTCCACTTCCTTGTCGTCGACCACTTCTAAGCCTCTGCTGGGTCCCACTCCTTTT
196 GCGAGGTTAATTCCACTTCCTTGTCGTCGACCACTTCTAAGCCTCTGCTGGGTCCCACTCCTTTT
*
367725 ATACTCAGGAAGCGCCTTAGGTCCGACGACGATAACGCCGGGAAGGACGATTCTAGTGGGCTCAC
261 ATACTCAGGAAGCGCCTCAGGTCCGACGACGATAACGCCGGGAAGGACGATTCTAGTGGGCTCAC
* *
367790 CGTTGGAGCAGGCGGCGTGCGGTCCATTGTGGGACCCGCGGGTACGCATACGCAT
326 CGTTGGACCAGGCGGCATGCGGTCCATTGTGGGACCCGCGGGTACGCATACGCAT
* *
367845 ACGGCCGTGGAAGGAGGATCAGGATGCCCATCATTTGTGCCGCTCGTGTCTTCCAGTTGATTTGC
1 ACGGCCGTGGAAGGAGGATCAGGATGCCCATCATTTGTGCCGCTCGTGTCTTCCAGTTGACTCGC
* *
367910 GAGTTGGGTCATAAATCCGACTGTGAAACCATTGAGTGGCTCTTGCGTCAGGCCGAACCTTCTAT
66 GAGTTGGGTCATAAATCCGAATGTCAAACCATTGAGTGGCTCTTGCGTCAGGCCGAACCTTCTAT
*
367975 CATAGCCACCACTGGCACCGGGACCACCCTCGCCAGCTTCTCCACCGTCTCGGTTTCCGTTCGCG
131 CATAGCCACCACTGGCACCGGGACCACCCCCGCCAGCTTCTCCACCGTCTCGGTTTCCGTTCGCG
*
368040 GCGGGGTTAATTCCACTTCCTTGTCGTCGACCACTTCTAAGCCTCTGCTGGGTCCCACTCCTTTT
196 GCGAGGTTAATTCCACTTCCTTGTCGTCGACCACTTCTAAGCCTCTGCTGGGTCCCACTCCTTTT
* *
368105 ATACTCGGGAAGCGCCTCAGGTCCGATGACGATAACGCCGGGAAGGACGATTCTAGTGGGCTCAC
261 ATACTCAGGAAGCGCCTCAGGTCCGACGACGATAACGCCGGGAAGGACGATTCTAGTGGGCTCAC
* *
368170 CGTTGGACCAGGCGGCATGGGGTCCATTGTGGTACCCGCGGGTACGCATACG
326 CGTTGGACCAGGCGGCATGCGGTCCATTGTGGGACCCGCGGGTACGCATACG
368222 AATGGGTTCT
Statistics
Matches: 359, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
380 359 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (380 bp):
ACGGCCGTGGAAGGAGGATCAGGATGCCCATCATTTGTGCCGCTCGTGTCTTCCAGTTGACTCGC
GAGTTGGGTCATAAATCCGAATGTCAAACCATTGAGTGGCTCTTGCGTCAGGCCGAACCTTCTAT
CATAGCCACCACTGGCACCGGGACCACCCCCGCCAGCTTCTCCACCGTCTCGGTTTCCGTTCGCG
GCGAGGTTAATTCCACTTCCTTGTCGTCGACCACTTCTAAGCCTCTGCTGGGTCCCACTCCTTTT
ATACTCAGGAAGCGCCTCAGGTCCGACGACGATAACGCCGGGAAGGACGATTCTAGTGGGCTCAC
CGTTGGACCAGGCGGCATGCGGTCCATTGTGGGACCCGCGGGTACGCATACGCAT
Found at i:372327 original size:21 final size:21
Alignment explanation
Indices: 372303--372343 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
372293 CAAGTTTGAA
*
372303 AATT-GGGATGCTTAATTTGGG
1 AATTAGGGAT-CTAAATTTGGG
372324 AATTAGGGATCTAAATTTGG
1 AATTAGGGATCTAAATTTGG
372344 CATAATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (21 bp):
AATTAGGGATCTAAATTTGGG
Found at i:372616 original size:2 final size:2
Alignment explanation
Indices: 372609--372670 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
372599 TAACCAAAAT
372609 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
372651 TA TA TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
372671 GATTTCAGAC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:375035 original size:27 final size:27
Alignment explanation
Indices: 374986--375038 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
374976 ATTAACATTT
*
374986 AAAAAATTGATTTAATTAATGATTAAAG
1 AAAAAATTGAGTTAATT-ATGATTAAAG
375014 AAAAAAGTTGAGTTAATT-TGATTAA
1 AAAAAA-TTGAGTTAATTATGATTAA
375039 TGGTAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 6 0.26
29 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (27 bp):
AAAAAATTGAGTTAATTATGATTAAAG
Found at i:375172 original size:16 final size:18
Alignment explanation
Indices: 375130--375173 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
375120 ACTAAATTAT
*
375130 TATATTAATATTAGTGCA
1 TATATTAATATTACTGCA
*
375148 TAAATTAATATTACT-CA
1 TATATTAATATTACTGCA
375165 T-TATTAATA
1 TATATTAATA
375174 ATTTAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.30
17 3 0.13
18 13 0.57
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATTAATATTACTGCA
Found at i:375226 original size:25 final size:27
Alignment explanation
Indices: 375166--375237 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 27
375156 TATTACTCAT
375166 TATTAATAATTTAATAATATTATATTTA
1 TATTAATAATTT-ATAATATTATATTTA
** *
375194 TAAAAATAATATATAATATTA-A-TTA
1 TATTAATAATTTATAATATTATATTTA
*
375219 TATTAATAATTTATTATAT
1 TATTAATAATTTATAATAT
375238 ATTACTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 18 0.49
26 1 0.03
27 9 0.24
28 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTAATAATTTATAATATTATATTTA
Found at i:375234 original size:16 final size:16
Alignment explanation
Indices: 375202--375239 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
375192 TATAAAAATA
375202 ATATATAATATTAATT
1 ATATATAATATTAATT
*
375218 ATAT-TAATAATTTATT
1 ATATATAAT-ATTAATT
375234 ATATAT
1 ATATAT
375240 TACTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 14 0.74
17 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATAATATTAATT
Found at i:375369 original size:19 final size:19
Alignment explanation
Indices: 375345--375398 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
375335 ATTACAAATT
375345 TTATTAAAATAATATTAAA
1 TTATTAAAATAATATTAAA
* *
375364 TTATTAAATTACTATTAAA
1 TTATTAAAATAATATTAAA
* *
375383 TAAATAAAATAATATT
1 TTATTAAAATAATATT
375399 TTTTGAGTGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATTAAAATAATATTAAA
Found at i:375658 original size:51 final size:51
Alignment explanation
Indices: 375582--375692 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
375572 CAAACACTAG
* * *
375582 AATATTTTCCAAATATCAATCAAATGAAAATGAAGA-AAACATTTTTTGAAA
1 AATATTTTCCAAATATCAAACAAATGAAAAGGAA-ACAAACATTTTTCGAAA
* * *
375633 AATATTTTTCGAATATCAAACAAATGAAAAGGAAACAAATATTTTTCGAAA
1 AATATTTTCCAAATATCAAACAAATGAAAAGGAAACAAACATTTTTCGAAA
375684 AATATTTTC
1 AATATTTTC
375693 TAATCAACCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (51 bp):
AATATTTTCCAAATATCAAACAAATGAAAAGGAAACAAACATTTTTCGAAA
Found at i:376042 original size:190 final size:190
Alignment explanation
Indices: 375711--376077 Score: 506
Period size: 190 Copynumber: 1.9 Consensus size: 190
375701 CAAACACACC
* *
375711 TTAAATAAACAAACCCTAAATTTCATCCGGTAAAAAATCTATTCATCCATTTTCTCTTAATCTCA
1 TTAAATAAACAAACCCTAAATTTCATCCGGCAAAAAACCTATTCATCCATTTTCTCTTAATCTCA
* * * * *
375776 CGCGGTTTGTGCCTTTGACCATCATCTCTCCATTGTTCTTCACCGATTCACACAGGATCGTAATA
66 CGCGGTTTATGCCTTTGACCATCATCTCTACAGTGATCTTCACCGATTCACACAGGATCGTAAGA
*
375841 GAAGTTTTCTTCAAGCTTCTAAATC-TTCTTGACAGTTAGCATCTTCAATGATTCACTTGT
131 GAAGCTTTCTTCAAGCTTCT-AATCTTTCTTGACAGTTAGCATCTTCAATGATTCACTTGT
* * *
375901 TTAAATGAACAAACCCTAAATTTTATCTGGCAAAAAACCTATTCAT-C-TTTTCTCTCTCAATCT
1 TTAAATAAACAAACCCTAAATTTCATCCGGCAAAAAACCTATTCATCCATTTTCTCT-T-AATCT
* * * * * * *
375964 CTCGTGGTTTATGCCTTTGACCATCATCTCTATAGTGATCTTTACTGATTCACACGGGATCGTAG
64 CACGCGGTTTATGCCTTTGACCATCATCTCTACAGTGATCTTCACCGATTCACACAGGATCGTAA
* *
376029 GAGAAGCTTTCTTCAAGTTTCTAATCTTTTTTGACAGTTAGCATCTTCA
129 GAGAAGCTTTCTTCAAGCTTCTAATCTTTCTTGACAGTTAGCATCTTCA
376078 GTTCTGCACT
Statistics
Matches: 154, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
188 8 0.05
189 6 0.04
190 140 0.91
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (190 bp):
TTAAATAAACAAACCCTAAATTTCATCCGGCAAAAAACCTATTCATCCATTTTCTCTTAATCTCA
CGCGGTTTATGCCTTTGACCATCATCTCTACAGTGATCTTCACCGATTCACACAGGATCGTAAGA
GAAGCTTTCTTCAAGCTTCTAATCTTTCTTGACAGTTAGCATCTTCAATGATTCACTTGT
Found at i:378358 original size:18 final size:18
Alignment explanation
Indices: 378335--378369 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
378325 ACTTTTACGA
378335 GATGTTTAATTGAGTGTC
1 GATGTTTAATTGAGTGTC
*
378353 GATGTTTAATTTAGTGT
1 GATGTTTAATTGAGTGT
378370 TATGACCATT
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:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (18 bp):
GATGTTTAATTGAGTGTC
Found at i:380381 original size:24 final size:24
Alignment explanation
Indices: 380349--380396 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
380339 CTAATTTTTC
380349 TTTTCCTAAGTGATAGATTATTGA
1 TTTTCCTAAGTGATAGATTATTGA
380373 TTTTCCTAAGTGATAGATTATTGA
1 TTTTCCTAAGTGATAGATTATTGA
380397 CATTGAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (24 bp):
TTTTCCTAAGTGATAGATTATTGA
Found at i:380434 original size:7 final size:7
Alignment explanation
Indices: 380422--380490 Score: 66
Period size: 7 Copynumber: 9.4 Consensus size: 7
380412 TTTCTTGCCC
380422 ATTTTTT
1 ATTTTTT
380429 ATTTTTT
1 ATTTTTT
380436 ATTATTTT
1 ATT-TTTT
*
380444 ATTATTT
1 ATTTTTT
380451 ATTATTATT
1 ATT-TT-TT
*
380460 ATTTATT
1 ATTTTTT
*
380467 ATTTATT
1 ATTTTTT
*
380474 ATTTATT
1 ATTTTTT
*
380481 ATTTATT
1 ATTTTTT
380488 ATT
1 ATT
380491 ATTATTATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
7 42 0.75
8 9 0.16
9 5 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTT
Found at i:380442 original size:10 final size:10
Alignment explanation
Indices: 380423--380502 Score: 76
Period size: 10 Copynumber: 8.0 Consensus size: 10
380413 TTCTTGCCCA
380423 TTTT-TTATT
1 TTTTATTATT
380432 TTTTATTA--
1 TTTTATTATT
380440 TTTTATTATT
1 TTTTATTATT
*
380450 TATTATTATT
1 TTTTATTATT
*
380460 ATTTATTATT
1 TTTTATTATT
*
380470 TATTATTTATT
1 TTTTA-TTATT
*
380481 ATTTATTATT
1 TTTTATTATT
380491 ATTATTATTATT
1 -TT-TTATTATT
380503 CTTAAATAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
8 8 0.14
9 4 0.07
10 28 0.49
11 9 0.16
12 8 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTATT
Found at i:380448 original size:3 final size:3
Alignment explanation
Indices: 380434--380502 Score: 86
Period size: 3 Copynumber: 21.7 Consensus size: 3
380424 TTTTTATTTT
380434 TTA TTA TT- TTA TTA TTTA TTA TTA TTA TTTA TTA TTTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA -TTA TTA -TTA TTA
380482 TTTA TTA TTA TTA TTA TTA TT
1 -TTA TTA TTA TTA TTA TTA TT
380503 CTTAAATAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.03
3 43 0.72
4 15 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:383463 original size:11 final size:11
Alignment explanation
Indices: 383447--383472 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
383437 TTTATTTTTC
383447 TATAACTTGTT
1 TATAACTTGTT
383458 TATAACTTGTT
1 TATAACTTGTT
383469 TATA
1 TATA
383473 TTGATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (11 bp):
TATAACTTGTT
Found at i:389145 original size:22 final size:22
Alignment explanation
Indices: 389118--389218 Score: 157
Period size: 22 Copynumber: 4.6 Consensus size: 22
389108 ACATCTACAT
* * *
389118 TCTTCAAAGATGATATATTATT
1 TCTTCAAAGATGATAGATTCTC
389140 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
389162 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
389184 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
389206 TTTTCAAATATGA
1 TCTTCAAAGATGA
389219 AAGCTTTATT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:390126 original size:141 final size:141
Alignment explanation
Indices: 389872--390130 Score: 446
Period size: 141 Copynumber: 1.8 Consensus size: 141
389862 GCCTACGGGT
*
389872 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAAACCAAGCCTTCGGGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAAACCAAGCCTTCAGGGGT
* * * *
389937 TTATTATTTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGTCTAACAAAGGGGTCTTGATTTGTAA
66 TTATTAATTATCTCAAAAGAGCTGTTAAAGAAAGATAAGCCTAACAAAGGGGTCTTGATTTGTAA
390002 GTCCCATGGGC
131 GTCCCATGGGC
* *
390013 CATCCATAAGACCTTCAGTGTAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCAGGGGT
1 CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAAACCAAGCCTTCAGGGGT
*
390078 TTATTAATTATCTCAAAAGAGTTGTTAAAGAAAGATAAGCCTAACAAAGGGGT
66 TTATTAATTATCTCAAAAGAGCTGTTAAAGAAAGATAAGCCTAACAAAGGGGT
390131 TCCTTGACAA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 110 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (141 bp):
CATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAAATTTTAGAAACCAAGCCTTCAGGGGT
TTATTAATTATCTCAAAAGAGCTGTTAAAGAAAGATAAGCCTAACAAAGGGGTCTTGATTTGTAA
GTCCCATGGGC
Found at i:391050 original size:24 final size:24
Alignment explanation
Indices: 391018--391079 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
391008 TGGGCAAAAT
391018 AAAAACACCAACGACAGAACAAGG
1 AAAAACACCAACGACAGAACAAGG
*
391042 AAAAACACCAACGGCAGAACAAGG
1 AAAAACACCAACGACAGAACAAGG
*
391066 AAAAACATCAACGA
1 AAAAACACCAACGA
391080 TGAACGAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.58, C:0.24, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAACACCAACGACAGAACAAGG
Found at i:391939 original size:11 final size:11
Alignment explanation
Indices: 391923--391957 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
391913 AAATTAGTAC
391923 TTTAATTATTA
1 TTTAATTATTA
391934 TTTAATTATTA
1 TTTAATTATTA
*
391945 TTTTATT-TTA
1 TTTAATTATTA
391955 TTT
1 TTT
391958 TAGTCATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:392291 original size:157 final size:156
Alignment explanation
Indices: 391991--392300 Score: 408
Period size: 157 Copynumber: 2.0 Consensus size: 156
391981 GATTAAATAA
* * *
391991 TAATATTTATTTATTTTTTAATATTAAGAAAGGGTTGTCTTAAATTAACCAGAGGTCATATTCTG
1 TAATATTTATTCATTTTTTAATATTAAGAAAGGGTTGTCTTAAAGTAACCAGAGGTCATATTATG
* * **
392056 ATATTTTTAAATAAATAAATATCTTACTTATAAAAACAAAAAAATATATATTTGTTTTAATTTTA
66 ATATTTTTAAATAAATAAATACCCTACTTATAAAAACAAAAAAATATATATTTACTTTAATTTTA
** *
392121 TTCAAATTA-TTTTTTTATTTTTTAT
131 TAAAAATAATTTTTTTTATTTTTTAT
* * * * *
392146 TAATATTTATTCATTTTTTAATATTGAAGAAAAGGGTTGTCTTAAAGTAACTATATGTCCTTTTA
1 TAATATTTATTCATTTTTTAATATT-AAG-AAAGGGTTGTCTTAAAGTAACCAGAGGTCATATTA
* ** *
392211 TGATATTTTTAAATAAATAAATACCCTATTTATAAAAACCTAAAAA-ATATATTTACTTTAGTTT
64 TGATATTTTTAAATAAATAAATACCCTACTTATAAAAACAAAAAAATATATATTTACTTTAATTT
392275 TATAAAAATAATTTTTTTTTATTTTT
129 TATAAAAATAA-TTTTTTTTATTTTT
392301 CCTCAAAATT
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
155 24 0.18
156 26 0.20
157 69 0.52
158 13 0.10
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (156 bp):
TAATATTTATTCATTTTTTAATATTAAGAAAGGGTTGTCTTAAAGTAACCAGAGGTCATATTATG
ATATTTTTAAATAAATAAATACCCTACTTATAAAAACAAAAAAATATATATTTACTTTAATTTTA
TAAAAATAATTTTTTTTATTTTTTAT
Found at i:395066 original size:37 final size:37
Alignment explanation
Indices: 394978--395121 Score: 143
Period size: 37 Copynumber: 3.8 Consensus size: 37
394968 ACACACATAT
* *
394978 ATATATTATATTATATAGTTTGC-AAAAGA-TTTTTGAAA
1 ATATA-TATAATATATAGTTT-CTAAAA-ACATTTTGAAA
*
395016 ATACGTATGTAATATATAGTTTCTAAAAACATTTTGAAA
1 ATA--TATATAATATATAGTTTCTAAAAACATTTTGAAA
* *
395055 ATATATATAATATATAATTTTTAAAAACACTTTTGAAA
1 ATATATATAATATATAGTTTCTAAAAACA-TTTTGAAA
* *
395093 AT-TGTATAATATATAGTTT-TTAAAACATT
1 ATATATATAATATATAGTTTCTAAAAACATT
395122 AATATATAGT
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
35 2 0.02
36 7 0.08
37 38 0.41
38 15 0.16
39 28 0.30
40 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (37 bp):
ATATATATAATATATAGTTTCTAAAAACATTTTGAAA
Found at i:395127 original size:22 final size:22
Alignment explanation
Indices: 395099--395143 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
395089 GAAAATTGTA
395099 TAATATATAGTTTTTAAAACAT
1 TAATATATAGTTTTTAAAACAT
395121 TAATATATAGTTTTTAAAACAT
1 TAATATATAGTTTTTAAAACAT
395143 T
1 T
395144 TTAGAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TAATATATAGTTTTTAAAACAT
Found at i:395132 original size:96 final size:97
Alignment explanation
Indices: 395025--395218 Score: 295
Period size: 96 Copynumber: 2.0 Consensus size: 97
395015 AATACGTATG
395025 TAATATATAGTTTCTAAAAACATTTT-GAAAATATATATAATATATAATTTTTAAAAACACTTTT
1 TAATATATAGTTT-TAAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAAACA-TTTT
**
395089 GAAAA-TTGTATAATATATAGTTTTT-AAAACAT
64 GAAAACTTACATAATATATAGTTTTTGAAAACAT
* * * *
395121 TAATATATAGTTTTTAAAACATTTTAGAAGATATATATAATATATAGTTTTTAAAACCATTTTGA
1 TAATATATAGTTTTAAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAAACATTTTGA
395186 AAACTTACATAATATATAGTTTTTGAAAACAT
66 AAACTTACATAATATATAGTTTTTGAAAACAT
395218 T
1 T
395219 TTTGAAAACT
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
95 20 0.22
96 61 0.69
97 8 0.09
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (97 bp):
TAATATATAGTTTTAAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAAACATTTTGA
AAACTTACATAATATATAGTTTTTGAAAACAT
Found at i:395160 original size:59 final size:59
Alignment explanation
Indices: 395062--395177 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 59
395052 AAAATATATA
*
395062 TAATATATAATTTTTAAAAACACTTTTGAAAATTGTATAATATATAGTTTTTAAAACAT
1 TAATATATAATTTTTAAAAACACTTTTGAAAATTATATAATATATAGTTTTTAAAACAT
* *
395121 TAATATATAGTTTTT-AAAACA-TTTTAGAAGATATATATAATATATAGTTTTTAAAAC
1 TAATATATAATTTTTAAAAACACTTTT-GAAAAT-TATATAATATATAGTTTTTAAAAC
395178 CATTTTGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
57 4 0.08
58 11 0.21
59 37 0.71
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (59 bp):
TAATATATAATTTTTAAAAACACTTTTGAAAATTATATAATATATAGTTTTTAAAACAT
Found at i:395171 original size:37 final size:37
Alignment explanation
Indices: 395121--395308 Score: 238
Period size: 37 Copynumber: 5.1 Consensus size: 37
395111 TTTAAAACAT
* *
395121 TAATATATAGTTTTTAAAACATTTTAGAAGA-TATATA
1 TAATATATAGTTTTTAAAACATTTTTGAAAACT-TATA
*
395158 TAATATATAGTTTTTAAAACCA-TTTTGAAAACTTACA
1 TAATATATAGTTTTTAAAA-CATTTTTGAAAACTTATA
395195 TAATATATAGTTTTTGAAAACATTTTTGAAAACTTATA
1 TAATATATAGTTTTT-AAAACATTTTTGAAAACTTATA
* ****
395233 TAATATATAGTTTTTGATTTTTTTTTGAAAACTTATA
1 TAATATATAGTTTTTAAAACATTTTTGAAAACTTATA
*
395270 TAATATATAATTTTTGAAAACATTTTTGAAAA-TTATA
1 TAATATATAGTTTTT-AAAACATTTTTGAAAACTTATA
395307 TA
1 TA
395309 GTTTTTAAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
37 84 0.64
38 47 0.36
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (37 bp):
TAATATATAGTTTTTAAAACATTTTTGAAAACTTATA
Found at i:395176 original size:133 final size:135
Alignment explanation
Indices: 394989--395247 Score: 362
Period size: 133 Copynumber: 1.9 Consensus size: 135
394979 TATATTATAT
* * *
394989 TATATAGTTTGCAAAAGATTTTTGAAAATACGTATGTAATATATAGTTTCTAAAAACATTTTGAA
1 TATATAGTTTGCAAAACATTTTAGAAAATAC-TATATAATATATAGTTTCTAAAAACATTTTGAA
* *
395054 AA-TATATATAATATATAATTTTTAAAAACACTTTTGAAAA-TTGTATAATATATAGTTTTTAAA
65 AACT-TACATAATATATAATTTTTAAAAACACTTTTGAAAACTTATATAATATATAGTTTTTAAA
395117 ACATTAA
129 ACATTAA
** * * *
395124 TATATAGTTTTTAAAACATTTTAGAAGATA-TATATAATATATAGTTTTTAAAACCATTTTGAAA
1 TATATAGTTTGCAAAACATTTTAGAAAATACTATATAATATATAGTTTCTAAAAACATTTTGAAA
* * *
395188 ACTTACATAATATATAGTTTTTGAAAACATTTTTGAAAACTTATATAATATATAGTTTTT
66 ACTTACATAATATATAATTTTTAAAAACACTTTTGAAAACTTATATAATATATAGTTTTT
395248 GATTTTTTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 64 0.59
134 20 0.18
135 25 0.23
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (135 bp):
TATATAGTTTGCAAAACATTTTAGAAAATACTATATAATATATAGTTTCTAAAAACATTTTGAAA
ACTTACATAATATATAATTTTTAAAAACACTTTTGAAAACTTATATAATATATAGTTTTTAAAAC
ATTAA
Found at i:395233 original size:75 final size:74
Alignment explanation
Indices: 395121--395308 Score: 261
Period size: 75 Copynumber: 2.5 Consensus size: 74
395111 TTTAAAACAT
* *
395121 TAATATATAGTTTTT-AAAACATTTTAGAAGATATATATAATATATAGTTTTTAAAACCATTTTG
1 TAATATATAGTTTTTGAAAACATTTTTGAAAAT-TATATAATATATAGTTTTTAAAACCATTTTG
395185 AAAACTTACA
65 AAAACTTACA
* *****
395195 TAATATATAGTTTTTGAAAACATTTTTGAAAACTTATATAATATATAGTTTTTGATTTTTTTTTG
1 TAATATATAGTTTTTGAAAACATTTTTGAAAA-TTATATAATATATAGTTTTTAAAACCATTTTG
*
395260 AAAACTTATA
65 AAAACTTACA
*
395270 TAATATATAATTTTTGAAAACATTTTTGAAAATTATATA
1 TAATATATAGTTTTTGAAAACATTTTTGAAAATTATATA
395309 GTTTTTAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 22 0.22
75 79 0.77
76 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (74 bp):
TAATATATAGTTTTTGAAAACATTTTTGAAAATTATATAATATATAGTTTTTAAAACCATTTTGA
AAACTTACA
Found at i:395350 original size:31 final size:32
Alignment explanation
Indices: 395286--395373 Score: 142
Period size: 32 Copynumber: 2.7 Consensus size: 32
395276 ATAATTTTTG
*
395286 AAAACATTTTTGAAAATTATATAGTTTTTAAA
1 AAAACATTTTTGAAAATTATATAGTTTTAAAA
395318 AAAACATTTATTGAAAATTATATAG-TTTAAAA
1 AAAACATTT-TTGAAAATTATATAGTTTTAAAA
395350 AAAACATTTTTGAAAATTTATATA
1 AAAACATTTTTGAAAA-TTATATA
395374 TAATATATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
31 7 0.13
32 31 0.58
33 15 0.28
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (32 bp):
AAAACATTTTTGAAAATTATATAGTTTTAAAA
Found at i:395382 original size:41 final size:38
Alignment explanation
Indices: 395334--395424 Score: 119
Period size: 41 Copynumber: 2.3 Consensus size: 38
395324 TTTATTGAAA
* *
395334 ATTATATAGTTTAAAAAAAACATTTTTGAAAATTTATAT
1 ATTATATAGTTTAAAAAAAACAGTTTTAAAAATTT-TAT
* *
395373 ATAATATATAATTTTAAAAAAACAGTTTTAAAAATTTTAT
1 AT--TATATAGTTTAAAAAAAACAGTTTTAAAAATTTTAT
395413 ATTATATAGTTT
1 ATTATATAGTTT
395425 TTTTAAACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 9 0.20
39 2 0.04
40 5 0.11
41 29 0.64
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (38 bp):
ATTATATAGTTTAAAAAAAACAGTTTTAAAAATTTTAT
Found at i:395456 original size:3 final size:3
Alignment explanation
Indices: 395448--395496 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
395438 TTTTTTATAT
*
395448 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA CTTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA
395495 TT
1 TT
395497 TTTTGTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:395497 original size:6 final size:6
Alignment explanation
Indices: 395439--395499 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
395429 AAACAATACT
* * * * * *
395439 TTTTTA TATTTA TTATTA TTATTA TTATTA TTATTA TTATTTA TTACTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TT-TTTA
395489 TTTTTA TTTTT
1 TTTTTA TTTTT
395500 TGTTTTAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
6 37 0.77
7 11 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:396568 original size:9 final size:9
Alignment explanation
Indices: 396554--396669 Score: 59
Period size: 9 Copynumber: 12.8 Consensus size: 9
396544 TTTAGTCATT
396554 TTTTATTTA
1 TTTTATTTA
396563 TTTTATTTA
1 TTTTATTTA
*
396572 TTTTATTCATT
1 TTTTATT--TA
396583 TTTTATTTAA
1 TTTTATTT-A
396593 CCTTTT-TTTA
1 --TTTTATTTA
396603 TTTTATTT-
1 TTTTATTTA
396611 TATTT-TTTA
1 T-TTTATTTA
*
396620 TTTT-TTGGA
1 TTTTATT-TA
396629 TTATTA-TTA
1 TT-TTATTTA
396638 TTGTT-TTT-
1 TT-TTATTTA
*
396646 TTCTATTTA
1 TTTTATTTA
396655 -TTTATTTA
1 TTTTATTTA
*
396663 TATTATT
1 TTTTATT
396670 ATTACGATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 30
0.69 0.07 0.25
Matches are distributed among these distances:
7 1 0.01
8 25 0.30
9 39 0.46
10 4 0.05
11 11 0.13
12 4 0.05
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:396623 original size:5 final size:5
Alignment explanation
Indices: 396554--396616 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
396544 TTTAGTCATT
* *
396554 TTTTA -TTTA TTTTA -TTTA TTTTA TTCATT- TTTTA TTTAA CCTTT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT--TTA TTTTA TTTTA -TTTTA
396598 TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
396617 TTATTTTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
4 13 0.28
5 28 0.60
6 4 0.09
7 2 0.04
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:396721 original size:38 final size:38
Alignment explanation
Indices: 396600--396722 Score: 103
Period size: 38 Copynumber: 3.3 Consensus size: 38
396590 TAACCTTTTT
* *
396600 TTATTTTATTTTAT-TTTT-TATTTT-T-TGGATTATTA
1 TTATTTTTTTTTATATTTTATATTTTATAT-CATTATTA
* * *
396635 TTATTGTTTTTTTCTA-TTTATTTATTTATATTATTATTA
1 TTATT-TTTTTTTATATTTTATAT-TTTATATCATTATTA
** * *
396674 CGATATTTTTTTATATTTTATATTTTATATCATTGTTA
1 TTATTTTTTTTTATATTTTATATTTTATATCATTATTA
396712 TTATTTTTTTT
1 TTATTTTTTTT
396723 GTTTTGTTCT
Statistics
Matches: 67, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
35 5 0.07
36 10 0.15
37 2 0.03
38 33 0.49
39 16 0.24
40 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (38 bp):
TTATTTTTTTTTATATTTTATATTTTATATCATTATTA
Found at i:399491 original size:90 final size:91
Alignment explanation
Indices: 399306--399501 Score: 268
Period size: 90 Copynumber: 2.1 Consensus size: 91
399296 AGATTATAAT
** *
399306 ATTATATATATACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTGGTTAAATGCCCCATCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGCTATCCCTCTAAAGCAA----TTAAACACCCCAGCTTTA
399371 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
61 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * * *
399402 ATTATAATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAA-TAAACACCTCGGCTTTATGGAT
1 ATTATAATATACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTAAACACCCCAGCTTTATGGAT
*
399466 AATATTCAGCTAGCCTGATAAAGGTG
66 AAGATTCAGCTAGCCTGATAAAGGTG
399492 ATTATAATAT
1 ATTATAATAT
399502 CTATACAATG
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
90 52 0.57
95 34 0.37
96 6 0.07
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (91 bp):
ATTATAATATACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTAAACACCCCAGCTTTATGGAT
AAGATTCAGCTAGCCTGATAAAGGTG
Found at i:400863 original size:110 final size:110
Alignment explanation
Indices: 400497--401135 Score: 501
Period size: 110 Copynumber: 5.5 Consensus size: 110
400487 GACACAATTT
* * * * * *
400497 ACTCGAGATTGGATCTCAACTTCACAACGAAGGATATTCAAGTCAAGGCTCAACTTCTCAACGAA
1 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACAACGAA
* *
400562 GGGGCCATCCATGATTTCAACTTCATGACGAAGGATATCTTGCCA
66 GGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCTTGCCA
* * * *** *
400607 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTTAACTTTATGGCCAT
1 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACAACGA-
*** * * * * *
400672 A-GTTTCATTCAGAGCCAATTTCAACTTCACGGCGAATGATAT-TGGACTCGAA
65 AGGGGCCA-TC-CA--CGATTTCAACTTCACGACGAAGGATATCTTG-C-C--A
* * * * *
400724 ACAATACAAGCTTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAAC
1 AC--T-CTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACAAC
*
400789 GAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCA
63 GAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCTTGCCA
* * ***
400837 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTTACGGTGAA
1 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACAACGAA
* * * * *
400902 TGGGCTTCCTAGTTTTATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTTG-AA
66 -GGG--GCC-------A-TC-CA--CGATTTCAACTTCACGACGAAGGATA-T---CTTGCCA
* ** * * *
400964 ACAATACAATCTTGGATTTCAACTTCACGACGAATGATATTCAAGTCAAGGCTCAACTTCACAAC
1 AC--T-CTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACAAC
* * *
401029 GAAGGGGCCATCCACGAGTTCAACTTCACAACGAAGGATATCGTGCCA
63 GAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCTTGCCA
* * *
401077 ACTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTTAACTTCAC
1 ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCAC
401136 GGCGAAGAGG
Statistics
Matches: 407, Mismatches: 86, Indels: 72
0.72 0.15 0.13
Matches are distributed among these distances:
110 155 0.38
111 8 0.02
112 4 0.01
113 10 0.02
114 23 0.06
115 3 0.01
116 47 0.12
117 4 0.01
118 2 0.00
119 6 0.01
120 54 0.13
121 2 0.00
122 1 0.00
124 24 0.06
125 1 0.00
127 5 0.01
128 3 0.01
129 4 0.01
130 51 0.13
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (110 bp):
ACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACAACGAA
GGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCTTGCCA
Found at i:401030 original size:240 final size:240
Alignment explanation
Indices: 400505--401303 Score: 1136
Period size: 240 Copynumber: 3.3 Consensus size: 240
400495 TTACTCGAGA
* * * *
400505 TTGGATCTCAACTTCACAACGAAGGATATTCAAGTCAAGGCTCAACTTCTCAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * *
400570 CCATGATTTCAACTTCATGACGAAGGATATCTTGCCAACTCTAGATTGGATTTCAACTTCACGAC
66 CCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTCAACTTCACGAC
*
400635 GAAGGATATCCAATTCAAAGCTTAAC-TT----T--AT-GGC--CATAGTTTCATTCAGAGCCAA
131 GAAGGATATCCAATTCAAAGCTTAACTTTACGGTGAATGGGCTTCCTAGTTTCATTCAGAGCCAA
* *
400690 TTTCAACTTCACGGCGAATGATATTGGACTCGAAACAATACAAGC
196 TTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAATC
400735 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
400800 CCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTCAACTTCACGAC
66 CCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTCAACTTCACGAC
* *
400865 GAAGGATATCCAATTCAAAGCTCAACTTTACGGTGAATGGGCTTCCTAGTTTTATTCAGAGCCAA
131 GAAGGATATCCAATTCAAAGCTTAACTTTACGGTGAATGGGCTTCCTAGTTTCATTCAGAGCCAA
*
400930 TTTCAACTTCACGGCGAAGGATATTGGACTTGAAACAATACAATC
196 TTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAATC
* *
400975 TTGGATTTCAACTTCACGACGAATGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * *
401040 CCACGAGTTCAACTTCACAACGAAGGATATCGTGCCAACTCTAGATTGGATTTCAACTTCACGAC
66 CCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTCAACTTCACGAC
* * * * *
401105 GAATGATATCCAATTCAAAGCTTAACTTCACGGCGAA-GAGGCTTCCCAGCTTCATTCAGAGCCA
131 GAAGGATATCCAATTCAAAGCTTAACTTTACGGTGAATG-GGCTTCCTAGTTTCATTCAGAGCCA
* * * * *
401169 GTTTTAACTTTACGGCGAAGGATATTGGACTCGAAGCAACATTC-ATC
195 ATTTCAACTTCACGGCGAAGGATATTGGACTCGAAAC-A-ATACAATC
* * *
401216 TTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGACTCAACTTCACAACGAAGG
1 ------TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGG
* *
401281 GACCATCCACGGTTTCAACTTCA
60 GGCCATCCACGATTTCAACTTCA
401304 TGAGGAACGG
Statistics
Matches: 511, Mismatches: 39, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
230 148 0.29
231 2 0.00
235 1 0.00
237 2 0.00
238 3 0.01
239 1 0.00
240 273 0.53
241 4 0.01
242 3 0.01
247 74 0.14
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (240 bp):
TTGGATTTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTCAACTTCACGAC
GAAGGATATCCAATTCAAAGCTTAACTTTACGGTGAATGGGCTTCCTAGTTTCATTCAGAGCCAA
TTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAATC
Found at i:401425 original size:124 final size:124
Alignment explanation
Indices: 401205--401454 Score: 358
Period size: 124 Copynumber: 2.0 Consensus size: 124
401195 GGACTCGAAG
*
401205 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGACTCAACTT
1 CAACATTCATCTTCAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGACTCAACTT
* * *
401270 CACAACGAAGGGACCATCCACGGTTTCAACTTCATGAGGAACGGA-ATCGTGCCCACCAA
66 CACAACGAAGGGACCATCCACGATTTCAACTTCACGAGGAA-GGATATCGTGCCCACAAA
* * * * *
401329 CAACATTCATCTTCAGATTGGATTTTAACTTCAGGACGAAGGATATCCAATTTAAGGCTCAACTT
1 CAACATTCATCTTCAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGACTCAACTT
* * * * *
401394 CACAACGAAGGGGCCCTCTACGATTTTAACTTCACGATGAAGGATATCGTGCCCACAAA
66 CACAACGAAGGGACCATCCACGATTTCAACTTCACGAGGAAGGATATCGTGCCCACAAA
401453 CA
1 CA
401455 GCAATGCCAT
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 3 0.03
124 108 0.97
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (124 bp):
CAACATTCATCTTCAGATTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGACTCAACTT
CACAACGAAGGGACCATCCACGATTTCAACTTCACGAGGAAGGATATCGTGCCCACAAA
Found at i:401641 original size:84 final size:84
Alignment explanation
Indices: 401500--401854 Score: 471
Period size: 84 Copynumber: 4.2 Consensus size: 84
401490 GATATCGTGT
* * * * *
401500 TCATTTGCAACATAACTCAAGGCAAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTCGACTA
1 TCATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
401565 CGCTTAGCTCCAAGGAACA
66 CGCTCAGCTCCAAGGCACA
* *
401584 TCATTTGCAGT-ATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAAAGATCTTCGAGTTCGACT
1 TCATTTGCA-TCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
401648 ATGCTCAGCTCCAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* * * *
401668 CCATTTGCATCATAGCTCAAGCCTAGAAGGGCTATCTGCC-ACCAAAAGACCTTCGAGTTCGACT
1 TCATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACT
* *
401732 ACACTCAGCTCCAAGGCATA
65 ACGCTCAGCTCCAAGGCACA
* * *
401752 TCATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACTTTTGAGTTCGACTA
1 TCATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
401817 AGCTCAACTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* *
401836 TCATTTGCAACATAGCTCA
1 TCATTTGCATCATAACTCA
401855 TGACAAGAAG
Statistics
Matches: 235, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
83 4 0.02
84 228 0.97
85 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (84 bp):
TCATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:401779 original size:168 final size:168
Alignment explanation
Indices: 401501--401894 Score: 558
Period size: 168 Copynumber: 2.3 Consensus size: 168
401491 ATATCGTGTT
* * *
401501 CATTTGCAACATAACTCAAGGCAAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTCGACTAC
1 CATTTGCAACATAGCTCAAGACAAGAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGACTAC
* *
401566 GCTTAGCTCCAAGGAACATCATTTGCAGTATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAAA
66 ACTCAGCTCCAAGGAACATCATTTGCAGTATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAAA
* *
401631 GA-TCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACAC
131 GACT-TTCGAGTTCGACTAAGCTCAACTCCAAGGCACAC
* * * * * *
401669 CATTTGCATCATAGCTCAAGCCTAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAACATAGCTCAAGACAAGAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGACTAC
* * * *
401734 ACTCAGCTCCAAGGCATATCATTTGCA-TCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAA
66 ACTCAGCTCCAAGGAACATCATTTGCAGT-ATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAA
* *
401798 AGACTTTTGAGTTCGACTAAGCTCAACTCCAAGGCACAT
130 AGACTTTCGAGTTCGACTAAGCTCAACTCCAAGGCACAC
* * *
401837 CATTTGCAACATAGCTCATGACAAGAAGGGCTATTTGTCAATAAAATACCTTCGAGTT
1 CATTTGCAACATAGCTCAAGACAAGAAGGGCTATTTGCCAACAAAATACCTTCGAGTT
401895 TGATTCCATT
Statistics
Matches: 197, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
167 1 0.01
168 195 0.99
169 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (168 bp):
CATTTGCAACATAGCTCAAGACAAGAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGACTAC
ACTCAGCTCCAAGGAACATCATTTGCAGTATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAAA
GACTTTCGAGTTCGACTAAGCTCAACTCCAAGGCACAC
Found at i:401894 original size:84 final size:84
Alignment explanation
Indices: 401500--401894 Score: 461
Period size: 84 Copynumber: 4.7 Consensus size: 84
401490 GATATCGTGT
* *
401500 TCATTTGCAACATAACTCAAGGCAAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
401565 CGCTTAGCTCCAAGGAACA
66 AGCTCAGCTCCAAGGCACA
** * * * *
401584 TCATTTGCAGTATAACTCAAGGCTAGAAGAGTTATCTGCCAACCAAAGATCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
*
401649 TGCTCAGCTCCAAGGCACA
66 AGCTCAGCTCCAAGGCACA
* * * * * * *
401668 CCATTTGCATCATAGCTCAAGCCTAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
*
401733 CA-CTCAGCTCCAAGGCATA
66 -AGCTCAGCTCCAAGGCACA
* * * *
401752 TCATTTGCATCATAACTCAAGGCTAGAAGGGTTATCTT-CCAACCAAAGACTTTTGAGTTCGACT
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTAT-TTGCCAACAAAAGACCTTCGAGTTCGACT
*
401816 AAGCTCAACTCCAAGGCACA
65 AAGCTCAGCTCCAAGGCACA
* * * * * * * *
401836 TCATTTGCAACATAGCTCATGACAAGAAGGGCTATTTGTCAATAAAATACCTTCGAGTT
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTT
401895 TGATTCCATT
Statistics
Matches: 261, Mismatches: 46, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
83 3 0.01
84 257 0.98
85 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (84 bp):
TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
AGCTCAGCTCCAAGGCACA
Found at i:402613 original size:37 final size:37
Alignment explanation
Indices: 402558--403025 Score: 412
Period size: 38 Copynumber: 12.6 Consensus size: 37
402548 TTGCAAACGG
*
402558 TTTTTGAAAATACATATATAATATATAGTTTCTAAAAACA
1 TTTTTGAAAAT---TATATAATATATAGTTTTTAAAAACA
*
402598 -TTTTGAAAATGTATATAATATATACTTTTTAAAAACA
1 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAAACA
* ** * *
402635 CTTTTGAAAGCTGTATAATATATAGTTTTT-ATAACA
1 TTTTTGAAAATTATATAATATATAGTTTTTAAAAACA
* * *
402671 TTTTAGAAGATATATATAATATATAGTTTTTAAAACCA
1 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAAACA
* * *
402709 -TTTTAAAAATTAAATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAATTATATAATATATAGTTTTTAAAAACA
* *
402745 TTTTTGAAGACTTATATAATATATAGTTTTTAAAACCA
1 TTTTTGAA-AATTATATAATATATAGTTTTTAAAAACA
* *
402783 -TTTTGAAAACTTAAATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAA-TTATATAATATATAGTTTTTAAAAACA
* *
402820 TTTTTGAAGACTTATATAATATATAGTTTTTGAAAACA
1 TTTTTGAA-AATTATATAATATATAGTTTTTAAAAACA
* *
402858 TTTTTGAAAACTTATATAATATATAATTTTTGAAAACA
1 TTTTTGAAAA-TTATATAATATATAGTTTTTAAAAACA
*
402896 TTTTTG--AA--A-AT--TATATAGTTTTTAAAAAACG
1 TTTTTGAAAATTATATAATATATAGTTTTT-AAAAACA
*
402927 TTTTT-----TTTTA-AATTATATAGTTTTTAAAAAACA
1 TTTTTGAAAATTATATAA-TATATAGTTTTT-AAAAACA
402960 TTTTTGAAAATTTATATATAATATATAGTTTTTTAAAAAACA
1 TTTTTGAAAA--T-TATATAATATATAG-TTTTT-AAAAACA
** * * *
403002 GATTTAAAAATTTTATATTATATA
1 TTTTTGAAAATTATATAATATATA
403026 AATTTTTTAA
Statistics
Matches: 356, Mismatches: 46, Indels: 53
0.78 0.10 0.12
Matches are distributed among these distances:
30 11 0.03
31 11 0.03
32 2 0.01
33 25 0.07
36 37 0.10
37 104 0.29
38 110 0.31
39 22 0.06
40 2 0.01
41 10 0.03
42 22 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAATTATATAATATATAGTTTTTAAAAACA
Found at i:402656 original size:74 final size:73
Alignment explanation
Indices: 402572--402912 Score: 434
Period size: 74 Copynumber: 4.6 Consensus size: 73
402562 TGAAAATACA
* * *
402572 TATATAATATATAGTTTCTAAAAACA-TTTTGAAAATGTATATAATATATACTTTTTAAAAACAC
1 TATATAATATATAGTTTTTGAAAACATTTTTGAAAAT-TATATAATATATAGTTTTTAAAAACA-
*
402636 TTTTGAAAGC
64 TTTTGAAAAC
* * * * *
402646 TGTATAATATATAGTTTTT-ATAACATTTTAGAAGATATATATAATATATAGTTTTTAAAACCAT
1 TATATAATATATAGTTTTTGAAAACATTTTTGAAAAT-TATATAATATATAGTTTTTAAAAACAT
* *
402710 TTTAAAAAT
65 TTTGAAAAC
* * *
402719 TAAATAATATATAGTTTTTGAAAACATTTTTGAAGACTTATATAATATATAGTTTTTAAAACCAT
1 TATATAATATATAGTTTTTGAAAACATTTTTGAA-AATTATATAATATATAGTTTTTAAAAACAT
402784 TTTGAAAAC
65 TTTGAAAAC
* * *
402793 TTAAATAATATATAGTTTTTGAAAACATTTTTGAAGACTTATATAATATATAGTTTTTGAAAACA
1 -TATATAATATATAGTTTTTGAAAACATTTTTGAA-AATTATATAATATATAGTTTTTAAAAACA
402858 TTTTTGAAAAC
64 -TTTTGAAAAC
*
402869 TTATATAATATATAATTTTTGAAAACATTTTTGAAAATTATATA
1 -TATATAATATATAGTTTTTGAAAACATTTTTGAAAATTATATA
402913 GTTTTTAAAA
Statistics
Matches: 238, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
73 29 0.12
74 95 0.40
75 71 0.30
76 43 0.18
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (73 bp):
TATATAATATATAGTTTTTGAAAACATTTTTGAAAATTATATAATATATAGTTTTTAAAAACATT
TTGAAAAC
Found at i:402863 original size:12 final size:12
Alignment explanation
Indices: 402846--402905 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
402836 TAATATATAG
402846 TTTTTGAAAACA
1 TTTTTGAAAACA
402858 TTTTTGAAAAC-
1 TTTTTGAAAACA
* *
402869 TTATAT-AATATATAA
1 TT-TTTGAA-A-A-CA
402884 TTTTTGAAAACA
1 TTTTTGAAAACA
402896 TTTTTGAAAA
1 TTTTTGAAAA
402906 TTATATAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
11 4 0.11
12 25 0.66
13 2 0.05
14 3 0.08
15 4 0.11
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:402998 original size:41 final size:40
Alignment explanation
Indices: 402940--403038 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 40
402930 TTTTTTAAAT
* ** *
402940 TATATAGTTTTTAAAAAACATTTTTGAAAATTTATATATAA
1 TATATAGTTTTTTAAAAACAGATTTAAAAATTT-TATATAA
*
402981 TATATAGTTTTTTAAAAAACAGATTTAAAAATTTTATATTA
1 TATATAGTTTTTT-AAAAACAGATTTAAAAATTTTATATAA
*
403022 TATA-AATTTTTTAAAAA
1 TATATAGTTTTTTAAAAA
403039 AATACTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
39 5 0.10
40 7 0.14
41 22 0.43
42 17 0.33
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (40 bp):
TATATAGTTTTTTAAAAACAGATTTAAAAATTTTATATAA
Found at i:403033 original size:102 final size:100
Alignment explanation
Indices: 402839--403023 Score: 228
Period size: 106 Copynumber: 1.8 Consensus size: 100
402829 ACTTATATAA
* * ** *
402839 TATATAGTTTTTGAAAACATTTTTGAAAACTTATATAATATATAATTTTTGAAAACATTTTTGAA
1 TATATAGTTTTTAAAAACATTTTTGAAAACTTATATAATATATAATTTTTAAAAACAGATTTAAA
*
402904 AATTATATAGTTTTTAAAAAACGTTTTTTTTTAAAT
66 AATTATATAG-TTATAAAAAACGTTTTTTTTTAAAT
* *
402940 TATATAGTTTTTAAAAAACATTTTTGAAAATTTATATATAATATATAGTTTTTTAAAAAACAGAT
1 TATATAGTTTTT-AAAAACATTTTTGAAAA-CT-TATATAATATATA-ATTTTT-AAAAACAGAT
*
403005 TTAAAAATTTTATA-TTATA
61 TTAAAAATTATATAGTTATA
403024 TAAATTTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
101 12 0.17
102 16 0.23
103 1 0.01
104 17 0.24
105 5 0.07
106 19 0.27
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (100 bp):
TATATAGTTTTTAAAAACATTTTTGAAAACTTATATAATATATAATTTTTAAAAACAGATTTAAA
AATTATATAGTTATAAAAAACGTTTTTTTTTAAAT
Found at i:403040 original size:41 final size:42
Alignment explanation
Indices: 402947--403039 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
402937 AATTATATAG
** * *
402947 TTTTTAAAAAACATTTTTGAAAATTTATATATAATATATAGT
1 TTTTTAAAAAACAGATTTAAAAATTTATATATAATATATAAT
*
402989 TTTTTAAAAAACAGATTTAAAAATTT-TATATTATATA-AAT
1 TTTTTAAAAAACAGATTTAAAAATTTATATATAATATATAAT
403029 TTTTTAAAAAA
1 TTTTTAAAAAA
403040 ATACTTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 13 0.28
41 10 0.22
42 23 0.50
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (42 bp):
TTTTTAAAAAACAGATTTAAAAATTTATATATAATATATAAT
Found at i:404180 original size:4 final size:4
Alignment explanation
Indices: 404171--404320 Score: 57
Period size: 4 Copynumber: 36.2 Consensus size: 4
404161 AATTTAGTCC
* *
404171 TTAT TTAT TTAT TTAT TTGTT TTAT TTATT TTAT TTAA TT-T TTAT TTAACCT
1 TTAT TTAT TTAT TTAT TT-AT TTAT TTA-T TTAT TTAT TTAT TTAT TT-A--T
* *
404223 TT-T TTATT TTAT TT-T TATTT TTAT TT-T TTGGAT TATAA TTAT TGT-T
1 TTAT TTA-T TTAT TTAT T-TAT TTAT TTAT TT--AT T-TAT TTAT T-TAT
* *
404269 TT-T TCTAT TTAT TTAT TTAT ATTA- TTA- TTAT GATAT TT-T TTAT TTTT
1 TTAT T-TAT TTAT TTAT TTAT -TTAT TTAT TTAT -TTAT TTAT TTAT TTAT
404316 TTAT T
1 TTAT T
404321 ATTGTTATTA
Statistics
Matches: 114, Mismatches: 11, Indels: 42
0.68 0.07 0.25
Matches are distributed among these distances:
3 22 0.19
4 61 0.54
5 25 0.22
6 2 0.02
7 4 0.04
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:404196 original size:9 final size:9
Alignment explanation
Indices: 404174--404334 Score: 69
Period size: 9 Copynumber: 18.3 Consensus size: 9
404164 TTAGTCCTTA
404174 TTTATTTA-
1 TTTATTTAT
*
404182 TTTATTTGT
1 TTTATTTAT
404191 TTTATTTAT
1 TTTATTTAT
404200 TTTATTTAATT
1 TTTATTT-A-T
*
404211 TTTATTTAACC
1 TTTATTT-A-T
404222 TTT-TTTAT
1 TTTATTTAT
404230 TTTATTT-T
1 TTTATTTAT
404238 TATT-TTTAT
1 T-TTATTTAT
*
404247 TTT-TTGGAT
1 TTTATT-TAT
* *
404256 TATAATTAT
1 TTTATTTAT
*
404265 TGT-TTT-T
1 TTTATTTAT
*
404272 TCTATTTA-
1 TTTATTTAT
404280 TTTATTTAT
1 TTTATTTAT
*
404289 ATTA-TTAT
1 TTTATTTAT
*
404297 TATGATATT-T
1 T-TTAT-TTAT
404307 TTTATTT-T
1 TTTATTTAT
404315 TTTA-TTAT
1 TTTATTTAT
404323 TGTTA-TTAT
1 T-TTATTTAT
404332 TTT
1 TTT
404335 TTGTTTTGTT
Statistics
Matches: 120, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.04
8 46 0.38
9 47 0.39
10 7 0.06
11 15 0.12
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTATTTAT
Found at i:404215 original size:11 final size:11
Alignment explanation
Indices: 404190--404242 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
404180 TATTTATTTG
404190 TTTTATTT-A-
1 TTTTATTTAAT
404199 TTTTATTTAAT
1 TTTTATTTAAT
404210 TTTTATTTAACCTT
1 TTTTATTTAA---T
*
404224 TTTTATTTTAT
1 TTTTATTTAAT
404235 TTTTATTT
1 TTTTATTT
404243 TTATTTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 8 0.21
10 1 0.03
11 19 0.50
14 10 0.26
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTTAAT
Found at i:404243 original size:11 final size:11
Alignment explanation
Indices: 404190--404250 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 11
404180 TATTTATTTG
404190 TTTTA-TTTA-
1 TTTTATTTTAT
*
404199 TTTTATTTAAT
1 TTTTATTTTAT
*
404210 TTTTATTTAACCTT
1 TTTTATTTTA---T
404224 TTTTATTTTAT
1 TTTTATTTTAT
404235 TTTTATTTTTAT
1 TTTTA-TTTTAT
404247 TTTT
1 TTTT
404251 TGGATTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
9 5 0.11
10 3 0.07
11 16 0.36
12 10 0.23
14 10 0.23
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:404251 original size:26 final size:26
Alignment explanation
Indices: 404174--404341 Score: 78
Period size: 26 Copynumber: 6.3 Consensus size: 26
404164 TTAGTCCTTA
*
404174 TTTA-TTTATTTATT-TGTTTTATTTAT
1 TTTATTTTATTT-TTAT-TTTTATTTTT
* * **
404200 TTTATTTAATTTTTA-TTTAACCTTT
1 TTTATTTTATTTTTATTTTTATTTTT
404225 TTTATTTTATTTTTATTTTTATTTTT
1 TTTATTTTATTTTTATTTTTATTTTT
* * *
404251 TGGATTATAATTATTGTTT-TTTCTA-TTTA
1 T---TTAT-TTTATT-TTTATTTTTATTTTT
* * * *
404280 TTTATTTATATTATTATTATGATATTT
1 TTTATTT-TATTTTTATTTTTATTTTT
*
404307 TTTATTTT-TTTATTATTGTTATTATTT
1 TTTATTTTATTT-TTATTTTTATT-TTT
*
404334 TTTGTTTT
1 TTTATTTT
404342 GTTCTTGGAT
Statistics
Matches: 105, Mismatches: 24, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
25 25 0.24
26 34 0.32
27 25 0.24
29 8 0.08
30 10 0.10
31 3 0.03
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTATTTTATTTTTATTTTTATTTTT
Found at i:404319 original size:23 final size:24
Alignment explanation
Indices: 404278--404322 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
404268 TTTTTCTATT
404278 TATTTATTTATATTATTATTATGA
1 TATTTATTTATATTATTATTATGA
* *
404302 TATTT-TTTATTTTTTTATTAT
1 TATTTATTTATATTATTATTAT
404323 TGTTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (24 bp):
TATTTATTTATATTATTATTATGA
Found at i:404319 original size:35 final size:34
Alignment explanation
Indices: 404226--404320 Score: 86
Period size: 35 Copynumber: 2.7 Consensus size: 34
404216 TTAACCTTTT
* *
404226 TTATT-TTATTTTTATTTTTATTTTTTGGATTATAA
1 TTATTGTT-TTTTTATTTTT-TTATTTAGATTATAA
* * *
404261 TTATTGTTTTTTCTATTTATTTATTTATATTATTA
1 TTATTGTTTTTT-TATTTTTTTATTTAGATTATAA
404296 TTA-TGATATTTTTTATTTTTTTATT
1 TTATTG-T-TTTTTTATTTTTTTATT
404321 ATTGTTATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
34 2 0.04
35 35 0.70
36 13 0.26
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.73
Consensus pattern (34 bp):
TTATTGTTTTTTTATTTTTTTATTTAGATTATAA
Found at i:404320 original size:29 final size:28
Alignment explanation
Indices: 404276--404341 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
404266 GTTTTTTCTA
404276 TTTATTTATTTATATTATTATTATGATATTT
1 TTTATTT-TTTATATTATTATTAT--TATTT
*
404307 TTTATTTTTT-TATTATTGTTATTATTT
1 TTTATTTTTTATATTATTATTATTATTT
*
404334 TTTGTTTT
1 TTTATTTT
404342 GTTCTTGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 12 0.36
29 11 0.33
30 3 0.09
31 7 0.21
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (28 bp):
TTTATTTTTTATATTATTATTATTATTT
Found at i:405686 original size:15 final size:15
Alignment explanation
Indices: 405668--405709 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
405658 ATGGCATTCT
405668 TTAAAACATTTTTAA
1 TTAAAACATTTTTAA
405683 TTAAAACATTTTTAA
1 TTAAAACATTTTTAA
405698 TTAAAACATTTT
1 TTAAAACATTTT
405710 CAAATGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAACATTTTTAA
Found at i:407164 original size:28 final size:29
Alignment explanation
Indices: 407105--407161 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
407095 AAGAATTAAT
*
407105 TTTAGTTAGTTTTTCTATTTATTTATTTTC
1 TTTAGTTA-TTTTTATATTTATTTATTTTC
*
407135 TTTAGTT-TTTTTATATTTCTTTCATTT
1 TTTAGTTATTTTTATATTTATTT-ATTT
407162 CTTATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 4 0.17
30 7 0.29
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (29 bp):
TTTAGTTATTTTTATATTTATTTATTTTC
Found at i:407643 original size:12 final size:12
Alignment explanation
Indices: 407621--407656 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
407611 AACATAGAGA
*
407621 ATTACTATTGTT
1 ATTATTATTGTT
*
407633 ATTATTTTTGTT
1 ATTATTATTGTT
407645 ATTATTATTGTT
1 ATTATTATTGTT
407657 TACTTCTCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.67
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:413026 original size:59 final size:60
Alignment explanation
Indices: 412959--413092 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 60
412949 AAGGACCAAA
* * * **
412959 TTAAAATAAGAGTCATAATTTAGGGAT-AAATTGAAATATTTAAAAGTTTTATGATTAAT
1 TTAAAATAAAAGTCATAATTTAGAGATAAAATTAAAATATTTAAAAGTTTTAAAATTAAT
* * *
413018 TTAAAATAAAAGTTATAGTTTAGAGATAAAATTAAAATATTTATAAGTTTTAAAATTAAT
1 TTAAAATAAAAGTCATAATTTAGAGATAAAATTAAAATATTTAAAAGTTTTAAAATTAAT
*
413078 TTAAAATAAATGTCA
1 TTAAAATAAAAGTCA
413093 GTTTAGAGAC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
59 23 0.36
60 41 0.64
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (60 bp):
TTAAAATAAAAGTCATAATTTAGAGATAAAATTAAAATATTTAAAAGTTTTAAAATTAAT
Found at i:413081 original size:29 final size:29
Alignment explanation
Indices: 412992--413085 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
412982 GGATAAATTG
* *
412992 AAATATTTAAAAGTTTTATGATTAATTTA
1 AAATATTTATAAGTTTTAAGATTAATTTA
* * *
413021 AAATAAAAGTTAT-AG-TTTAGAGATAAAATTA
1 AAAT---ATTTATAAGTTTTA-AGATTAATTTA
*
413052 AAATATTTATAAGTTTTAAAATTAATTTA
1 AAATATTTATAAGTTTTAAGATTAATTTA
413081 AAATA
1 AAATA
413086 AATGTCAGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 5 0.10
29 19 0.38
30 8 0.16
31 14 0.28
32 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (29 bp):
AAATATTTATAAGTTTTAAGATTAATTTA
Found at i:414156 original size:32 final size:32
Alignment explanation
Indices: 414083--414188 Score: 137
Period size: 32 Copynumber: 3.4 Consensus size: 32
414073 TCATACCTAG
* *
414083 CGTTCACTTTTTG-TTTAGTTTTAGTA-CCCGT
1 CGTTAACTTTTTGTTTTA-TTTTAGTATCCCGC
*
414114 TGTTAACTTTTTGTTTTATTTTAGTATCCCGC
1 CGTTAACTTTTTGTTTTATTTTAGTATCCCGC
* *
414146 CGTTAACTTTTTGTTTCATTTTAGTATCCCAC
1 CGTTAACTTTTTGTTTTATTTTAGTATCCCGC
414178 CGTTAA-TTTTT
1 CGTTAACTTTTT
414189 AACGACGGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
31 24 0.36
32 43 0.64
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (32 bp):
CGTTAACTTTTTGTTTTATTTTAGTATCCCGC
Found at i:414442 original size:98 final size:99
Alignment explanation
Indices: 414255--414449 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 99
414245 AATGAAAGTT
* *
414255 TAAATACTAAAACGAAATAAAAGTGATAATTCATATACAAAGTGTATATTTTACCTTAAAAATAA
1 TAAATACTAAAACAAAATAAAAGTGATAATTCATATACAAAGTGTATATTTTACCCTAAAAATAA
414320 TCACTGAACTAAACAAATGATCATATAACTATTC
66 TCACTGAACTAAACAAATGATCATATAACTATTC
* * *
414354 TAAATATTAAAACAAAATAAAAGTGATAATTTATATACTAAA-TGTGTA-TTTACCCTAAAAATA
1 TAAATACTAAAACAAAATAAAAGTGATAATTCATATAC-AAAGTGTATATTTTACCCTAAAAATA
414417 ATCACTGAACTAAACAAATGATCATATAACTAT
65 ATCACTGAACTAAACAAATGATCATATAACTAT
414450 CCTATCTAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
98 47 0.52
99 40 0.44
100 3 0.03
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (99 bp):
TAAATACTAAAACAAAATAAAAGTGATAATTCATATACAAAGTGTATATTTTACCCTAAAAATAA
TCACTGAACTAAACAAATGATCATATAACTATTC
Found at i:419270 original size:27 final size:25
Alignment explanation
Indices: 419219--419270 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
419209 ACTTTGTTTC
*
419219 TCTTTTCTTTCTTGCTTTGATTTTG
1 TCTTTTCTTTCTTGCTTTCATTTTG
*
419244 TCTTTTCTTTTACTTTCTTTCATTTTG
1 TCTTTTC-TTT-CTTGCTTTCATTTTG
419271 CATGTTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 3 0.13
27 13 0.57
ACGTcount: A:0.06, C:0.17, G:0.08, T:0.69
Consensus pattern (25 bp):
TCTTTTCTTTCTTGCTTTCATTTTG
Found at i:432269 original size:2 final size:2
Alignment explanation
Indices: 432262--432288 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
432252 AACATAACAT
432262 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
432289 GATTTTATTA
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:435800 original size:23 final size:22
Alignment explanation
Indices: 435774--435816 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
435764 TATAAAAAAT
435774 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
435797 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
435817 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:438388 original size:34 final size:34
Alignment explanation
Indices: 438345--438413 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
438335 ATGGACACTC
438345 ATCAACATTCCTACAAATGTTTTTCACAATTCAT
1 ATCAACATTCCTACAAATGTTTTTCACAATTCAT
438379 ATCAACATTCCTACAAATGTTTTTCACAATTCAT
1 ATCAACATTCCTACAAATGTTTTTCACAATTCAT
438413 A
1 A
438414 CCATGTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (34 bp):
ATCAACATTCCTACAAATGTTTTTCACAATTCAT
Found at i:440642 original size:45 final size:46
Alignment explanation
Indices: 440554--440642 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
440544 TTGAAAAAGC
* *
440554 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGAA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGAA
440600 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATG
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATG
440643 CATTCGATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 20 0.49
46 21 0.51
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGAA
Found at i:441074 original size:19 final size:20
Alignment explanation
Indices: 441036--441075 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
441026 TTTGAAATTA
*
441036 CTCCCCCTTACTATAACATTT
1 CTCCCCCTTA-TAAAACATTT
441057 CTCCCCCTT-TAAAACATTT
1 CTCCCCCTTATAAAACATTT
441076 TACACTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCCCCCTTATAAAACATTT
Found at i:448899 original size:17 final size:19
Alignment explanation
Indices: 448871--448919 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
448861 TGTGCATCGA
448871 TGCATCAAATGCACTG-A-G
1 TGCATC-AATGCACTGTATG
* *
448889 TGCATCGATGCATTGTATG
1 TGCATCAATGCACTGTATG
448908 TGCATCAATGCA
1 TGCATCAATGCA
448920 TAAAATGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.27
18 7 0.27
19 12 0.46
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (19 bp):
TGCATCAATGCACTGTATG
Found at i:448926 original size:45 final size:46
Alignment explanation
Indices: 448838--448928 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
448828 TTGAAAAAGC
* * * *
448838 CTGAGTGTATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
*
448884 CTGAGTGCATCGATGCATTGT-ATGTGCATCAATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
448929 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
Found at i:448976 original size:20 final size:20
Alignment explanation
Indices: 448948--448986 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
448938 CAAGAAATTA
448948 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
448968 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
448987 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:452266 original size:24 final size:24
Alignment explanation
Indices: 452238--452284 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
452228 ATCAGCATCA
* *
452238 CCTTGAACACTAGAATCTGCACCT
1 CCTTGAACACTAAAACCTGCACCT
*
452262 CCTTGAGCACTAAAACCTGCACC
1 CCTTGAACACTAAAACCTGCACC
452285 AACATGACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (24 bp):
CCTTGAACACTAAAACCTGCACCT
Found at i:454833 original size:20 final size:20
Alignment explanation
Indices: 454808--454870 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
454798 AATCATATTG
454808 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
454828 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATT-CCC
*
454849 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
454869 CC
1 CC
454871 TGTCTAACGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 22 0.54
21 19 0.46
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Done.