Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 19
Found at i:410325 original size:60 final size:60
Alignment explanation
Indices: 410230--410410 Score: 197
Period size: 60 Copynumber: 3.0 Consensus size: 60
410220 ATTATATGTT
*
410230 CTCAAACTATGA-TTCTCATTTTAAATTAGTTCTTAAACTTTTGAATATTCCAATTTCATC
1 CTCAAACTATGACTT-TCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
** * * * *
410290 CTCAAACTATGACTTTTGTTTTAAATTAGTCCTTAAACTTTTAAATGTTCCAATGTAATC
1 CTCAAACTATGACTTTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
** * * * *
410350 GC-CAAACTATGACCCTCATTCTAGATTGGTACC-CAAACTTTTGAATATTCCAATTTCATC
1 -CTCAAACTATGACTTTCATTTTAAATTAGT-CCTTAAACTTTTGAATATTCCAATTTCATC
410410 C
1 C
410411 CCACATTTAT
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 1 0.01
60 93 0.94
61 5 0.05
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (60 bp):
CTCAAACTATGACTTTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
Found at i:410667 original size:61 final size:61
Alignment explanation
Indices: 410553--410689 Score: 145
Period size: 61 Copynumber: 2.3 Consensus size: 61
410543 AGAATTAAGA
* *
410553 TCATAGTTTGAGGATGAAAATGAAATCTTCAAAAGTTTGAGGATTAATTTAGAAAAAATAG
1 TCATAGTTTGAGGATGAAAATGAAATATTCAAAAGTTTGAGGATTAATATAGAAAAAATAG
* * * ** * *
410614 TCATAGTTT-AGGGATGAAATTGAATTATTTAAAAGTTT-AGGGATTGGTATAG-AATAAGAG
1 TCATAGTTTGA-GGATGAAAATGAAATATTCAAAAGTTTGA-GGATTAATATAGAAAAAATAG
*
410674 TCATAATTTGAGGATG
1 TCATAGTTTGAGGATG
410690 CTTTTGCAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
60 21 0.33
61 42 0.67
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.34
Consensus pattern (61 bp):
TCATAGTTTGAGGATGAAAATGAAATATTCAAAAGTTTGAGGATTAATATAGAAAAAATAG
Found at i:410847 original size:29 final size:30
Alignment explanation
Indices: 410786--410854 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
410776 ACCAAAAATA
*
410786 ATTTTTTTGTAACAATAAGGATCTAAAATT
1 ATTTTTTTGTAACAATAAGGATCTAAAAGT
* *
410816 ATTTTTTTGTCAA-AATAAGTA-CTTAAAGT
1 ATTTTTTTGT-AACAATAAGGATCTAAAAGT
*
410845 ATTATTTTGT
1 ATTTTTTTGT
410855 TGCAATAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.44
30 17 0.50
31 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (30 bp):
ATTTTTTTGTAACAATAAGGATCTAAAAGT
Found at i:414297 original size:26 final size:26
Alignment explanation
Indices: 414261--414327 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
414251 TTGGACCCTT
414261 AGTGCATCGGTGCATCAAATGCACTG
1 AGTGCATCGGTGCATCAAATGCACTG
414287 AGTGCATCGGTGCATCAAATGCACTG
1 AGTGCATCGGTGCATCAAATGCACTG
* *
414313 AGTGCAACGATGCAT
1 AGTGCATCGGTGCAT
414328 GGTATGTGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (26 bp):
AGTGCATCGGTGCATCAAATGCACTG
Found at i:415433 original size:74 final size:75
Alignment explanation
Indices: 415263--415466 Score: 241
Period size: 75 Copynumber: 2.7 Consensus size: 75
415253 TGTACAAGGG
* * * * *
415263 GGGGGGAATCGGTACCCCCT-TGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCAGAACA
1 GGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAACA
** *
415327 AAACTGTTTA
66 AAACCATTCA
** * * *
415337 GGGGGGAATCCTTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAACA
415402 AAACCATTCA
66 AAACCATTCA
* *
415412 -GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 GGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
415467 TTTTTGGCTT
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
74 35 0.32
75 45 0.41
76 30 0.27
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (75 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAACA
AAACCATTCA
Found at i:416096 original size:17 final size:17
Alignment explanation
Indices: 416074--416116 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
416064 TCATAAATCC
*
416074 AAAATCCAATAATCCAA
1 AAAATCCAACAATCCAA
*
416091 AAAATCAAACAATCCAA
1 AAAATCCAACAATCCAA
*
416108 AATATCCAA
1 AAAATCCAA
416117 AATGTTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATCCAACAATCCAA
Found at i:416108 original size:9 final size:8
Alignment explanation
Indices: 416068--416118 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
416058 CACCATTCAT
416068 AAATCC-A
1 AAATCCAA
416075 AAATCCAA
1 AAATCCAA
*
416083 TAATCCAAA
1 AAATCC-AA
416092 AAAT-CAA
1 AAATCCAA
416099 ACAATCCAA
1 A-AATCCAA
416108 AATATCCAA
1 AA-ATCCAA
416117 AA
1 AA
416119 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 9 0.24
8 11 0.30
9 17 0.46
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.16
Consensus pattern (8 bp):
AAATCCAA
Found at i:423317 original size:74 final size:76
Alignment explanation
Indices: 423147--423352 Score: 274
Period size: 75 Copynumber: 2.7 Consensus size: 76
423137 CCGTTGTACA
* * * * * *
423147 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCATTCTGGAAATCTCGGAA
** *
423211 CAAAACTGTTT
66 CAAAACCATTC
*
423222 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCTGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCATTCTGGAAATCTCGGAA
*
423286 CCAAACCATTC
66 CAAAACCATTC
*
423297 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCTGAGCATTCTGGAA
423353 TTTTTGGCTT
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
74 21 0.18
75 63 0.54
76 32 0.28
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCATTCTGGAAATCTCGGAA
CAAAACCATTC
Found at i:423600 original size:84 final size:83
Alignment explanation
Indices: 423500--423667 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 83
423490 AGTTATATCG
* *
423500 AATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCATTTAACTTAATTTGTTATATCGAAAT
1 AATATACTTAGAAAATCATTTGAAAAATCTTAAAATCCATTTAACTTAATTTGTTATATCGAAAC
423565 ATCAAAATGTTTT-AACA
66 ATCAAAATGTTTTCAACA
*
423582 AATATACTTTTAGAAAATCATTTGAAAAATCTTAAAATTCATTTAACTTAATTTGTTATATCGAA
1 AATATAC--TTAGAAAATCATTTGAAAAATCTTAAAATCCATTTAACTTAATTTGTTATATCGAA
423647 ACATCAAAATGTTTTCAACA
64 ACATCAAAATGTTTTCAACA
423667 A
1 A
423668 TCTCCCCCTT
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
82 7 0.09
84 68 0.85
85 5 0.06
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (83 bp):
AATATACTTAGAAAATCATTTGAAAAATCTTAAAATCCATTTAACTTAATTTGTTATATCGAAAC
ATCAAAATGTTTTCAACA
Found at i:424094 original size:15 final size:15
Alignment explanation
Indices: 424060--424094 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
424050 AAATAAAAGT
*
424060 TCAAATATCCATCAA
1 TCAAATATCCAACAA
*
424075 ACAAATATCCAACAA
1 TCAAATATCCAACAA
424090 TCAAA
1 TCAAA
424095 GAAAGACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (15 bp):
TCAAATATCCAACAA
Found at i:426159 original size:44 final size:44
Alignment explanation
Indices: 426070--426166 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
426060 GCTCTTGTGC
* *
426070 ATCGATGCACATTCAAGGGCGTGCATCGGTGCATCAGATGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGATAATGT
* * *
426114 ATCGATGCACATTCAAAGGG-ATGCATTGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGATAA-TGT
426158 ATCGATGCA
1 ATCGATGCA
426167 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGATAATGT
Found at i:432031 original size:20 final size:19
Alignment explanation
Indices: 432006--432059 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
431996 AAAAGCCTGA
432006 GTGCATCGATGCATAGTATT
1 GTGCATCGATGCATAGTA-T
*
432026 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAGTAT
**
432045 ACGCATCGATGCATA
1 GTGCATCGATGCATA
432060 AAATGCATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATAGTAT
Found at i:432095 original size:84 final size:83
Alignment explanation
Indices: 431963--432124 Score: 204
Period size: 84 Copynumber: 1.9 Consensus size: 83
431953 CACTAAGAGT
** *
431963 GCATCAATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATAGTATT-G
1 GCATCAATGCATAAAATGCATTCGATGTTAAGAAAAA-CCTGAGTGCATCGATGCAT-GGATTGG
432027 TGCATCGATGCATGGTATAC
64 TGCATCGATGCATGGTATAC
* *
432047 GCATCGATGCATAAAATGCATTCGATGTTCAAGAAATTAA-TTGA-TGCATCGATGCATGGATTG
1 GCATCAATGCATAAAATGCATTCGATGTT-AAGAAA--AACCTGAGTGCATCGATGCATGGATTG
*
432110 GTGCATCGGTGCATG
63 GTGCATCGATGCATG
432125 CCCTTGAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
83 4 0.06
84 55 0.81
85 7 0.10
87 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (83 bp):
GCATCAATGCATAAAATGCATTCGATGTTAAGAAAAACCTGAGTGCATCGATGCATGGATTGGTG
CATCGATGCATGGTATAC
Found at i:432114 original size:20 final size:20
Alignment explanation
Indices: 432086--432124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
432076 CAAGAAATTA
432086 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
432106 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
432125 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:433589 original size:30 final size:31
Alignment explanation
Indices: 433555--433634 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
433545 CATCTTTAGA
*
433555 TTTTAATAATTGTAATAT-TTTTATGTAATG
1 TTTTAATAATTGTAATATGTTTAATGTAATG
* * *
433585 TTTTAATATTTCT-TTATGTTTAATGTAATG
1 TTTTAATAATTGTAATATGTTTAATGTAATG
433615 TTTT--TAATTG-AATATAGTTT
1 TTTTAATAATTGTAATAT-GTTT
433635 TTTATTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 7 0.17
29 7 0.17
30 26 0.65
ACGTcount: A:0.30, C:0.01, G:0.10, T:0.59
Consensus pattern (31 bp):
TTTTAATAATTGTAATATGTTTAATGTAATG
Found at i:436795 original size:19 final size:18
Alignment explanation
Indices: 436759--436797 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
436749 TCTTAACCTA
* *
436759 AAAAACCCTAAGTTGCTC
1 AAAAACCCTAAATGGCTC
436777 AAAAACCCTAAAATGGCTC
1 AAAAACCCT-AAATGGCTC
436796 AA
1 AA
436798 CCAACCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (18 bp):
AAAAACCCTAAATGGCTC
Found at i:444002 original size:81 final size:81
Alignment explanation
Indices: 443867--444029 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
443857 AGAGCGGCGG
*
443867 CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACTGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
1 CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACGGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
443932 AGTATCACAACCGGAA
66 AGTATCACAACCGGAA
* *
443948 CAAAGGCGTAGAGGGCCATGAAAGCCTAGTTGACGGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
1 CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACGGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
*
444013 AGTATCACAACTGGAA
66 AGTATCACAACCGGAA
444029 C
1 C
444030 GCATTGGAGG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACGGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
AGTATCACAACCGGAA
Found at i:450021 original size:3 final size:3
Alignment explanation
Indices: 450013--450038 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
450003 ATGTCATATA
450013 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
450039 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:454036 original size:14 final size:14
Alignment explanation
Indices: 454013--454042 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
454003 TCATTCATTT
454013 TTTTAATATTTTTA
1 TTTTAATATTTTTA
*
454027 TTTTATTATTTTTA
1 TTTTAATATTTTTA
454041 TT
1 TT
454043 AATTATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTAATATTTTTA
Found at i:454047 original size:13 final size:13
Alignment explanation
Indices: 454009--454049 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
453999 TCGTTCATTC
454009 ATTTTT-TTAA-T
1 ATTTTTATTAATT
*
454020 ATTTTTATTTTATT
1 ATTTTTA-TTAATT
454034 ATTTTTATTAATT
1 ATTTTTATTAATT
454047 ATT
1 ATT
454050 AAATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
13 11 0.44
14 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTTATTAATT
Found at i:454087 original size:11 final size:14
Alignment explanation
Indices: 454029--454089 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 14
454019 TATTTTTATT
454029 TTATTATTT--TTA
1 TTATTATTTAATTA
*
454041 TTAATTATTAAATT-
1 TT-ATTATTTAATTA
*
454055 TAATTATTTAATTA
1 TTATTATTTAATTA
454069 TTATTATTTAA-TA
1 TTATTATTTAATTA
454082 TATATTAT
1 T-TATTAT
454090 ATATTTTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.05
13 19 0.47
14 17 0.43
15 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATTTAATTA
Found at i:457317 original size:19 final size:19
Alignment explanation
Indices: 457281--457317 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
457271 TGAAAATGAT
*
457281 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
457300 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
457318 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:459861 original size:19 final size:19
Alignment explanation
Indices: 459834--459880 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
459824 TGGTCTCAAA
*
459834 TCAATATTCTAACTTAAAT
1 TCAACATTCTAACTTAAAT
459853 TCAACATTCTAACTTAAAT
1 TCAACATTCTAACTTAAAT
459872 TCAACATTC
1 TCAACATTC
459881 AATAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAACATTCTAACTTAAAT
Found at i:459891 original size:19 final size:21
Alignment explanation
Indices: 459843--459902 Score: 81
Period size: 19 Copynumber: 3.0 Consensus size: 21
459833 ATCAATATTC
459843 TAACTTAAATTCAACATTC--
1 TAACTTAAATTCAACATTCAA
459862 TAACTTAAATTCAACATTCAA
1 TAACTTAAATTCAACATTCAA
* *
459883 TAA-TTAATTTCCACATTCAA
1 TAACTTAAATTCAACATTCAA
459903 CACCCTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 19 0.51
20 15 0.41
21 3 0.08
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
TAACTTAAATTCAACATTCAA
Found at i:460777 original size:20 final size:20
Alignment explanation
Indices: 460752--460806 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
460742 AATTTCACTA
460752 CTAAATTTCACTGTTTCATT
1 CTAAATTTCACTGTTTCATT
460772 CTAAATTTCACTGTTTCATT
1 CTAAATTTCACTGTTTCATT
*
460792 CTAAATTTCATTGTT
1 CTAAATTTCACTGTT
460807 CCAAAATGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.51
Consensus pattern (20 bp):
CTAAATTTCACTGTTTCATT
Found at i:463995 original size:55 final size:54
Alignment explanation
Indices: 463957--464373 Score: 500
Period size: 55 Copynumber: 7.6 Consensus size: 54
463947 AACGAGCCTA
* * *
463957 CTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTG
1 CTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCA-AAAACGGGTCCG
* * *
464012 CTCCCTATTCGTTCAGGGAGTATA-ATACTTGAACAATCTTCAATAAACGGGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-AAACGGGTCCG
* * *
464067 CTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCCG
* * * *
464122 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAATGGGTCCA
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCCG
*
464177 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCCG
* * ** *
464232 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACATGTTCG
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCCG
* * * *
464287 CTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAATGGGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCCG
464342 CTCCCTATT-CTATCAGAGAGTATAGAACTCGA
1 CTCCCTATTCCT-TCAGAGAGTATAGAACTCGA
464374 TCTTCATAAA
Statistics
Matches: 322, Mismatches: 31, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
54 5 0.02
55 312 0.97
56 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (54 bp):
CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACGGGTCCG
Found at i:464089 original size:110 final size:110
Alignment explanation
Indices: 463957--464373 Score: 581
Period size: 110 Copynumber: 3.8 Consensus size: 110
463947 AACGAGCCTA
* *
463957 CTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCCCTAT
1 CTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCTGCTCCCTAT
* * * * *
464020 TCGTTCAGGGAGTATA-ATACTTGAACAATCTTCAATAAACGGGTCCG
64 TCCTTCAGAGAGTATAGA-ACTCGAATAATCTTCAACAAACGGGTCCG
* * *
464067 CTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCTCTATTC
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCCCTATTC
* *
464132 CTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAATGGGTCCA
66 CTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACGGGTCCG
* * *
464177 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTC
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCCCTATTC
** *
464242 CTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACATGTTCG
66 CTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACGGGTCCG
* * *
464287 CTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAATGGGTCTGCTCCCTATT-
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCCCTATTC
464351 CTATCAGAGAGTATAGAACTCGA
66 CT-TCAGAGAGTATAGAACTCGA
464374 TCTTCATAAA
Statistics
Matches: 279, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
109 2 0.01
110 274 0.98
111 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (110 bp):
CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCCCTATTC
CTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAACGGGTCCG
Found at i:464213 original size:165 final size:165
Alignment explanation
Indices: 463961--464373 Score: 563
Period size: 165 Copynumber: 2.5 Consensus size: 165
463951 AGCCTACTCC
* *
463961 CTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCCCTATTCGT
1 CTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAATGGGTCTGCTCCCTATTCCT
* * * *
464024 TCAGGGAGTATA-ATACTTGAACAATCTTCA-ATAAACGGGTCCGCTCCCTATTCGTTCAGGGAG
64 TCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAG
*
464087 TATAGAACTCGAACAATCTTCATA-AAAC-GGGTCTGCTCT
127 TATAGAACTCGAACAATCTTCA-ACAAACAGGTTC-GCTCT
* ** *
464126 CTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCA-ACAAATGGGTCCACTCTCTATTCCTT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAATGGGTCTGCTCCCTATTCCTT
*
464190 CAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT
65 CAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTAT
* *
464255 AGAACTCGAATAATCTTCAACAAACATGTTCGCTCT
130 AGAACTCGAACAATCTTCAACAAACAGGTTCGCTCT
*
464291 CTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCATAAAATGGGTCTGCTCCCTATT-CTAT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCTGCTCCCTATTCCT-T
464355 CAGAGAGTATAGAACTCGA
65 CAGAGAGTATAGAACTCGA
464374 TCTTCATAAA
Statistics
Matches: 220, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
164 4 0.02
165 208 0.95
166 8 0.04
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (165 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCTGCTCCCTATTCCTTC
AGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
GAACTCGAACAATCTTCAACAAACAGGTTCGCTCT
Found at i:464478 original size:37 final size:36
Alignment explanation
Indices: 464390--464495 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 36
464380 TAAAATGAGT
* * *
464390 TTGCTTCACTACTCTTCTGTGAAGGCTTATGATGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGAA
*
464426 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAG-ATGAA
* *
464463 TTGCTTCACTGCTCTTTCGTGAAGGCTTAAGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
464496 TAACCTGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 30 0.48
37 32 0.52
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGAA
Found at i:465800 original size:7 final size:7
Alignment explanation
Indices: 465780--465925 Score: 61
Period size: 7 Copynumber: 19.1 Consensus size: 7
465770 CCCCCTTTTA
465780 TTTC-TT
1 TTTCTTT
465786 TTTC-TT
1 TTTCTTT
465792 TTTCTTTT
1 TTTC-TTT
465800 TTCATCATTT
1 TT--TC-TTT
465810 TTTCATTTT
1 TTTC--TTT
465819 TTTCTCTT
1 TTTCT-TT
465827 TCTTCTTT
1 T-TTCTTT
465835 TTTCTTT
1 TTTCTTT
465842 TTT-TATT
1 TTTCT-TT
465849 TTT-TATT
1 TTTCT-TT
*
465856 TTT-TAT
1 TTTCTTT
*
465862 TTTATTT
1 TTTCTTT
465869 TTTCTTCT
1 TTTCTT-T
*
465877 TTT-TCT
1 TTTCTTT
465883 TTTCATTT
1 TTTC-TTT
465891 TTCATCATTT
1 TT--TC-TTT
465901 TTCTCTTTT
1 TT-TC-TTT
465910 TTTCTTT
1 TTTCTTT
465917 TTTCATTT
1 TTTC-TTT
465925 T
1 T
465926 CATTTTTTTC
Statistics
Matches: 116, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
6 19 0.16
7 38 0.33
8 26 0.22
9 18 0.16
10 15 0.13
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:465821 original size:33 final size:33
Alignment explanation
Indices: 465784--465947 Score: 113
Period size: 33 Copynumber: 5.2 Consensus size: 33
465774 CTTTTATTTC
465784 TTTTTCTTTTTCTTTTTTCATCATTTTTTCATT
1 TTTTTCTTTTTCTTTTTTCATCATTTTTTCATT
* * *
465817 TTTTTCTCTTTCTTCTTTT-TTC-TTTTTTTA-T
1 TTTTTCTTTTTCTT-TTTTCATCATTTTTTCATT
* *
465848 TTTTT-ATTTT-TTATTT--T-ATTTTTTC-TT
1 TTTTTCTTTTTCTTTTTTCATCATTTTTTCATT
*
465875 CTTTTTC-TTTTCATTTTTCATCATTTTTCTC-TT
1 -TTTTTCTTTTTCTTTTTTCATCATTTTT-TCATT
* *
465908 TTTTTCTTTTT-TCATTTTCAT--TTTTTTCATCA
1 TTTTTCTTTTTCT-TTTTTCATCATTTTTTCAT-T
465940 TTTTTCTT
1 TTTTTCTT
465948 CAAGCAAAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
27 8 0.08
28 12 0.11
29 6 0.06
30 5 0.05
31 13 0.12
32 27 0.26
33 30 0.29
34 4 0.04
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (33 bp):
TTTTTCTTTTTCTTTTTTCATCATTTTTTCATT
Found at i:475652 original size:45 final size:47
Alignment explanation
Indices: 475576--475686 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 47
475566 CCATGCTTTG
475576 TTATTCACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-
1 TTATTCA-AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA
* * * *
475623 TTGTTCAAAAAATAAA-CCTAACCGTATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA
475669 TTTATTCAAAAAACGAAA
1 -TTATTCAAAAAA-GAAA
475687 ATAAATGACT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 27 0.49
46 8 0.15
47 17 0.31
48 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (47 bp):
TTATTCAAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:483032 original size:2 final size:2
Alignment explanation
Indices: 483025--483050 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
483015 GAGGAGGAAA
483025 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
483051 GGAATAAAAA
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:487914 original size:25 final size:25
Alignment explanation
Indices: 487886--487934 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
487876 TTTATTTTCT
487886 TTTTCTATAAAATTCTT-TAAATTTA
1 TTTTCTATAAAATT-TTATAAATTTA
*
487911 TTTTCTCTAAAATTTTATAAATTT
1 TTTTCTATAAAATTTTATAAATTT
487935 TAAATTAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTCTATAAAATTTTATAAATTTA
Found at i:493099 original size:42 final size:43
Alignment explanation
Indices: 493040--493126 Score: 158
Period size: 42 Copynumber: 2.0 Consensus size: 43
493030 GACTTAAACA
493040 TGAAATAGAAGCTCCAAGTTATCTCTCAA-TTTTTGCTTCATT
1 TGAAATAGAAGCTCCAAGTTATCTCTCAATTTTTTGCTTCATT
*
493082 TGAAATAGAAGCTCCAAGTTTTCTCTCAATTTTTTGCTTCATT
1 TGAAATAGAAGCTCCAAGTTATCTCTCAATTTTTTGCTTCATT
493125 TG
1 TG
493127 GCGATGAGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (43 bp):
TGAAATAGAAGCTCCAAGTTATCTCTCAATTTTTTGCTTCATT
Found at i:493311 original size:32 final size:32
Alignment explanation
Indices: 493270--493339 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
493260 GTTTTTGGTT
* * ** *
493270 AGATGAAAGGAATTTTTTGTGTAGGAGATTGA
1 AGATGAAAGGAATGTGTAATGTAAGAGATTGA
*
493302 AGATGAAAGGAGTGTGTAATGTAAGAGATTGA
1 AGATGAAAGGAATGTGTAATGTAAGAGATTGA
493334 AGATGA
1 AGATGA
493340 TGTGCACAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.29
Consensus pattern (32 bp):
AGATGAAAGGAATGTGTAATGTAAGAGATTGA
Found at i:493875 original size:6 final size:6
Alignment explanation
Indices: 493864--493897 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
493854 TTCATTGTAG
493864 ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA ATAG
1 ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA ATAG
493898 GGGAATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
ATAGAA
Found at i:494142 original size:29 final size:29
Alignment explanation
Indices: 494081--494142 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
494071 GGGGGTAGGT
** **
494081 CGCCATGCACGCCCAGTGACCTACCAGGT
1 CGCCATGCACGCCCAACGACCTACCAGCA
494110 CGCCATGCACGCCCAACGACCT-CCATGCA
1 CGCCATGCACGCCCAACGACCTACCA-GCA
494139 CGCC
1 CGCC
494143 CAGCTCGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (29 bp):
CGCCATGCACGCCCAACGACCTACCAGCA
Found at i:494342 original size:29 final size:28
Alignment explanation
Indices: 494300--494383 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
494290 TGCAACGTGG
494300 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
494329 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
*
494358 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCC-AGGGATCCCAGCGAC
494384 CTATGCCTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (28 bp):
GTAGGTCGCCAGGGATCCCAGCGACATT
Found at i:494866 original size:27 final size:29
Alignment explanation
Indices: 494803--494866 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
494793 ATATATTAAA
494803 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
494832 -AAT-TTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
494857 AAATAGTTAA
1 AAATAATTAA
494867 GTTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 1 0.03
26 11 0.37
27 15 0.50
28 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:494959 original size:34 final size:36
Alignment explanation
Indices: 494891--494960 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
494881 GTTGAATTTA
494891 TATTATATAAAAATTAGTTTATTAGTAGTTTAAGTTT
1 TATTATATAAAAATTAGTTTATTA-TAGTTTAAGTTT
494928 TATTATAATAAAAA-TAGTTTA-T-TAGTTTAAGTT
1 TATTAT-ATAAAAATTAGTTTATTATAGTTTAAGTT
494961 ATATAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 11 0.34
36 1 0.03
37 13 0.41
38 7 0.22
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (36 bp):
TATTATATAAAAATTAGTTTATTATAGTTTAAGTTT
Found at i:495000 original size:26 final size:25
Alignment explanation
Indices: 494971--495031 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
494961 ATATAAAAGA
* *
494971 ATAATTATTTAAATTAGTTTATTGTT
1 ATAATTAGTT-AATTAGTTTATTATT
494997 ATAAATTAGTTAATTAGTTTATTATT
1 AT-AATTAGTTAATTAGTTTATTATT
495023 ATAAATTAG
1 AT-AATTAG
495032 GGTAAAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.52
Consensus pattern (25 bp):
ATAATTAGTTAATTAGTTTATTATT
Found at i:495031 original size:18 final size:17
Alignment explanation
Indices: 494972--495017 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
494962 TATAAAAGAA
494972 TAATTATTTAAATTAGT
1 TAATTATTTAAATTAGT
* *
494989 TTATTGTTATAAATTAGT
1 TAATTATT-TAAATTAGT
495007 TAATTAGTTTA
1 TAATTA-TTTA
495018 TTATTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (17 bp):
TAATTATTTAAATTAGT
Found at i:495298 original size:29 final size:29
Alignment explanation
Indices: 495266--495351 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
495256 TTTAGTAGTA
495266 AATTATAATTAAAAATCA-TTTATTAGTTT
1 AATTATAATTAAAAAT-AGTTTATTAGTTT
*
495295 AATT-TATATTAAGAATAGTTTATTAG-TT
1 AATTATA-ATTAAAAATAGTTTATTAGTTT
*
495323 ACGTTAT-ATTAAAGAATAGTTTATTAGTT
1 A-ATTATAATTAAA-AATAGTTTATTAGTT
495352 GTTTAAGGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
28 11 0.23
29 35 0.73
30 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (29 bp):
AATTATAATTAAAAATAGTTTATTAGTTT
Found at i:496664 original size:23 final size:24
Alignment explanation
Indices: 496624--496669 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
496614 TTTAATTATT
*
496624 ATTTAAATTAACTATATT-ATTTG
1 ATTTAAATAAACTATATTGATTTG
* *
496647 ATTTAAATAAATTTTATTGATTT
1 ATTTAAATAAACTATATTGATTT
496670 TGTAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAAATAAACTATATTGATTTG
Found at i:497678 original size:14 final size:14
Alignment explanation
Indices: 497659--497706 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
497649 TTCAAGTCGT
497659 AAATCATTACTATC
1 AAATCATTACTATC
497673 AAATCATTAC--T-
1 AAATCATTACTATC
*
497684 AAATCATTAATATC
1 AAATCATTACTATC
497698 AAATCATTA
1 AAATCATTA
497707 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:497686 original size:25 final size:25
Alignment explanation
Indices: 497658--497706 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
497648 GTTCAAGTCG
*
497658 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
497683 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
497707 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:497722 original size:21 final size:22
Alignment explanation
Indices: 497658--497716 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
497648 GTTCAAGTCG
*
497658 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
497681 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
497705 TAAAT-ATTAATA
1 TAAATCATTAATA
497717 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:497727 original size:21 final size:22
Alignment explanation
Indices: 497658--497727 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
497648 GTTCAAGTCG
* *
497658 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
497683 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
497705 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
497726 TA
1 TA
497728 TTACTAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:497852 original size:49 final size:54
Alignment explanation
Indices: 497675--498432 Score: 705
Period size: 60 Copynumber: 13.4 Consensus size: 54
497665 TTACTATCAA
* * *
497675 ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTAT-TATT
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-AATT-TCTACT
*
497730 ACTAATTACT-AATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACT
1 A-TCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
*
497788 AATCATTACTAAATCATTACTATCAAATCATTAAAATTTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
497848 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
* *
497908 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC-A-T
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCTACT
*
497961 -T-ATTA-TTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
* *
498017 AATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
*
498077 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
* *
498137 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC-A-T
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCTACT
498190 -T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
*
498246 AATCATTACTAAATCATTACTATCAAATCATT-AAAATTAATAATTTCATTAT-TACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAA--TAATT-TCTACT
498302 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-----TACT
* *
498362 AATCATTACT--ATCAAATTACTATTAAATCATTAAATATTAATAATAA-TT-T-C-
1 -ATCATTACTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCTACT
498413 ATCATTACT-AATCATTACTA
1 ATCATTACTAAATCATTACTA
498433 AATCTTATAA
Statistics
Matches: 634, Mismatches: 24, Indels: 96
0.84 0.03 0.13
Matches are distributed among these distances:
49 84 0.13
50 19 0.03
51 5 0.01
52 2 0.00
53 7 0.01
54 14 0.02
55 27 0.04
56 45 0.07
57 11 0.02
58 15 0.02
59 45 0.07
60 355 0.56
61 4 0.01
62 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (54 bp):
ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCTACT
Found at i:497920 original size:120 final size:120
Alignment explanation
Indices: 497674--498436 Score: 1164
Period size: 120 Copynumber: 6.6 Consensus size: 120
497664 ATTACTATCA
*
497674 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT-A--A
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
497735 TTACT-AATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
497788 AATCATTACTAAATCATTACTATCAAATCATTAAA-ATTTAATAATAATTTCATTATTACTAATC
1 AATCATTACTAAATCATTAATATCAAATCATTAAATA-TTAATAATAATTTCATTATTACTAATC
497852 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
65 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
497908 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC---ATTA-T--T-A
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
497966 -T--T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* * *
498017 AATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
498082 TTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
498137 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTC------A-T--T-A
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
498192 TTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
498246 AATCATTACTAAATCATTACTATCAAATCATTAAA-A-T--TAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
498307 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* * *
498362 AATCATTACT--ATCAAATTACTATTAAATCATTAAATATTAATAATAATTTCATCATTACTAAT
1 AATCATTACTAAATC--ATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
498425 CATTACTAAATC
64 CATTACTAAATC
498437 TTATAAATAC
Statistics
Matches: 599, Mismatches: 14, Indels: 66
0.88 0.02 0.10
Matches are distributed among these distances:
105 10 0.02
107 1 0.00
108 1 0.00
109 179 0.30
110 7 0.01
111 2 0.00
112 6 0.01
113 4 0.01
114 52 0.09
115 16 0.03
116 81 0.14
117 6 0.01
118 7 0.01
119 22 0.04
120 204 0.34
121 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (120 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:497972 original size:109 final size:109
Alignment explanation
Indices: 497859--498432 Score: 821
Period size: 109 Copynumber: 5.1 Consensus size: 109
497849 ATCATTACTA
497859 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
497924 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
66 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
497968 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
* * *
498033 TTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACT
66 TTAATATCAAATCATTAAATATTAATAATAATTTC---ATTA-T--T-A-T--T
*
498087 AAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
1 -AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
*
498152 ATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
65 ATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
498197 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
* * * *
498262 TTACTATCAAATCATTAAA-ATTAATAATTTCATTATTACTAATCATTACTA
66 TTAATATCAAATCATTAAATATTAATAA--T-A--ATT--TCATTATTA-TT
498313 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT--ATCA
1 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC-
* * * *
498376 AATTACTATTAAATCATTAAATATTAATAATAATTTCATCATTACT
65 -ATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
498422 AATCATTACTA
1 AATCATTACTA
498433 AATCTTATAA
Statistics
Matches: 425, Mismatches: 18, Indels: 44
0.87 0.04 0.09
Matches are distributed among these distances:
108 8 0.02
109 190 0.45
110 10 0.02
111 1 0.00
112 7 0.02
113 5 0.01
114 5 0.01
115 9 0.02
116 80 0.19
117 13 0.03
119 1 0.00
120 96 0.23
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (109 bp):
AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATT
Found at i:498031 original size:46 final size:48
Alignment explanation
Indices: 497912--498035 Score: 180
Period size: 49 Copynumber: 2.6 Consensus size: 48
497902 ATTACTAATC
* *
497912 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATT-ACATCAAATCATTAAAAATTAATAATAATTTCATT
*
497962 ATTATTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATT
498011 ATTACTAATCATTAC-T-AAATCATTA
1 ATTACTAATCATTACATCAAATCATTA
498036 TTATCAAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 9 0.13
47 1 0.01
48 1 0.01
49 53 0.77
50 5 0.07
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:498043 original size:229 final size:228
Alignment explanation
Indices: 497674--498432 Score: 1314
Period size: 229 Copynumber: 3.3 Consensus size: 228
497664 ATTACTATCA
*
497674 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATTAC
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-AATT-TCA-T--T-ATTAC
497739 TAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
60 TAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
497803 ATTACTATCAAATCATTAAAATTTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
125 ATTACTATCAAATCATTAAAA-TTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAC
497868 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
189 TATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
497908 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
497973 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATT
66 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
* *
498038 ATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTAAATCATTAATATCAA
131 ATCAAATCATT-AAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAA
498103 ATCATTAAAAATTAATAATAATTTCATTATTACT
195 ATCATTAAAAATTAATAATAATTTCATTATTACT
498137 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
498202 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
66 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
498267 ATCAAATCATTAAAA-T--TAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAA
131 ATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAA
498329 TCATTAAAAATTAATAATAATTTCATTATTACT
196 TCATTAAAAATTAATAATAATTTCATTATTACT
* * *
498362 AATCATTACT--ATCAAATTACTATTAAATCATTAAATATTAATAATAATTTCATCATTACTAAT
1 AATCATTACTAAATC--ATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
498425 CATTACTA
64 CATTACTA
498433 AATCTTATAA
Statistics
Matches: 509, Mismatches: 12, Indels: 17
0.95 0.02 0.03
Matches are distributed among these distances:
223 3 0.01
225 140 0.28
227 1 0.00
228 30 0.06
229 279 0.55
230 4 0.01
231 1 0.00
232 2 0.00
233 4 0.01
234 45 0.09
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (228 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACT
ATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAA
TCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:498054 original size:24 final size:24
Alignment explanation
Indices: 498006--498054 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
497996 AATAATAATT
* *
498006 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
498030 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
498054 T
1 T
498055 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:498262 original size:11 final size:11
Alignment explanation
Indices: 498240--498323 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
498230 TAATTTCATT
498240 ATTACT-AATC
1 ATTACTAAATC
498250 ATTACTAAATC
1 ATTACTAAATC
498261 ATTACTATCAAATC
1 ATTAC--T-AAATC
*
498275 ATTA--AAATTA
1 ATTACTAAA-TC
* * ** *
498285 ATAATTTCATT
1 ATTACTAAATC
498296 ATTACT-AATC
1 ATTACTAAATC
498306 ATTACTAAATC
1 ATTACTAAATC
498317 ATTACTA
1 ATTACTA
498324 TCAAATCATT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.05
10 18 0.32
11 25 0.44
12 1 0.02
13 1 0.02
14 9 0.16
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:502269 original size:29 final size:29
Alignment explanation
Indices: 502236--502320 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
502226 GGTCGCCGGT
* *
502236 AGGTCGCCGGGATTGCTTGGCGACCTACA
1 AGGTCGCTGGGAGTGCTTGGCGACCTACA
* * ***
502265 AGGTCACTGGGAGTGCATGGCGACCTTGT
1 AGGTCGCTGGGAGTGCTTGGCGACCTACA
*
502294 AGGTCGCTTGGAGTGCTTGGCGACCTA
1 AGGTCGCTGGGAGTGCTTGGCGACCTA
502321 TGGTTGGGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (29 bp):
AGGTCGCTGGGAGTGCTTGGCGACCTACA
Found at i:502367 original size:12 final size:12
Alignment explanation
Indices: 502350--502374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
502340 CCATGCACGA
502350 CACGATCCTCGT
1 CACGATCCTCGT
502362 CACGATCCTCGT
1 CACGATCCTCGT
502374 C
1 C
502375 GGAAGCCACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (12 bp):
CACGATCCTCGT
Found at i:503406 original size:2 final size:2
Alignment explanation
Indices: 503399--503461 Score: 110
Period size: 2 Copynumber: 31.5 Consensus size: 2
503389 TTGAAAATGA
503399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
503441 AT AT AT AT AT AT GAT -T AT AT A
1 AT AT AT AT AT AT -AT AT AT AT A
503462 CAAATTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:507266 original size:21 final size:21
Alignment explanation
Indices: 507240--507280 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
507230 GGTCCATTTT
507240 TTATTTAACACTTTAACAGTG
1 TTATTTAACACTTTAACAGTG
507261 TTATTTAACACTTTAACAGT
1 TTATTTAACACTTTAACAGT
507281 TAGGGATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (21 bp):
TTATTTAACACTTTAACAGTG
Found at i:507342 original size:23 final size:23
Alignment explanation
Indices: 507309--507384 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
507299 GGAATGTGAG
*
507309 ATTTTCATGAGAATGAAATCTAC
1 ATTTTCCTGAGAATGAAATCTAC
507332 ATTTTCCTGAGAATGAAATCTAC
1 ATTTTCCTGAGAATGAAATCTAC
*
507355 ATTTCCCTGAGAATGAAATCTAC
1 ATTTTCCTGAGAATGAAATCTAC
507378 ATTTTCC
1 ATTTTCC
507385 CGTTTGGTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (23 bp):
ATTTTCCTGAGAATGAAATCTAC
Found at i:507964 original size:20 final size:19
Alignment explanation
Indices: 507935--507975 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
507925 AGTAATTTTA
*
507935 TTTCCTGATAATCTTATAT
1 TTTCCTGATAATCTTACAT
507954 TTTCACTGATAATCTTACAT
1 TTTC-CTGATAATCTTACAT
507974 TT
1 TT
507976 CGTACCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTCCTGATAATCTTACAT
Found at i:511237 original size:30 final size:30
Alignment explanation
Indices: 511188--511248 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
511178 ATTGATTTTC
*
511188 TAAAAAATAATTTATGTAAAATAAATTATT
1 TAAAAAATAATTTACGTAAAATAAATTATT
* *
511218 TAAAAATTATTTTACGTAAAATAAATTATT
1 TAAAAAATAATTTACGTAAAATAAATTATT
511248 T
1 T
511249 TATGGTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAAAAATAATTTACGTAAAATAAATTATT
Found at i:512169 original size:34 final size:37
Alignment explanation
Indices: 512125--512226 Score: 149
Period size: 34 Copynumber: 2.8 Consensus size: 37
512115 TAGGGTCCTA
*
512125 CTAGGATTCAAACTCTTAAAAATATGATAGA-A-TTT
1 CTAGGATTCAAACTCTTAAAAATAGGATAGACATTTT
512160 -TAGGATTCAAACTCTTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCTTAAAAATAGGATAGACATTTT
*
512195 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCTTAAAAATAGGATAGA
512227 GTTCTACTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
35 3 0.05
37 27 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (37 bp):
CTAGGATTCAAACTCTTAAAAATAGGATAGACATTTT
Found at i:512656 original size:18 final size:17
Alignment explanation
Indices: 512617--512659 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
512607 ATTATATGGA
512617 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
512633 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
512651 TATTATTAT
1 TATTATTAT
512660 ATGTGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:512910 original size:2 final size:2
Alignment explanation
Indices: 512905--512937 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
512895 CTTATAACTT
512905 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
512938 TATTTGCGTT
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:514312 original size:16 final size:17
Alignment explanation
Indices: 514293--514326 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
514283 ACCTTACTAA
*
514293 CTCTTTTTATTT-TTTC
1 CTCTCTTTATTTATTTC
514309 CTCTCTTTATTTATTTC
1 CTCTCTTTATTTATTTC
514326 C
1 C
514327 ATCACTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (17 bp):
CTCTCTTTATTTATTTC
Found at i:515718 original size:8 final size:8
Alignment explanation
Indices: 515705--515743 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
515695 GAACATTTCA
*
515705 TGCATTCT
1 TGCATTTT
515713 TGCA-TTT
1 TGCATTTT
515720 TGCATTTT
1 TGCATTTT
*
515728 TGCCTTTT
1 TGCATTTT
515736 TGCATTTT
1 TGCATTTT
515744 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:516861 original size:8 final size:7
Alignment explanation
Indices: 516840--516918 Score: 68
Period size: 7 Copynumber: 10.3 Consensus size: 7
516830 TCCAATCAAG
516840 AAGAAAA
1 AAGAAAA
516847 AAGAAAA
1 AAGAAAA
516854 AAGCAAAA
1 AAG-AAAA
*
516862 AAAAAAA
1 AAGAAAA
*
516869 AAAAAACA
1 AAGAAA-A
516877 AAGAAAA
1 AAGAAAA
516884 AAGAGAAA
1 AAGA-AAA
516892 CAAGAACATA
1 -AAGAA-A-A
*
516902 AGGAAAAA
1 AAG-AAAA
516910 AAGAAAA
1 AAGAAAA
516917 AA
1 AA
516919 ACAAGAATCA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
7 31 0.51
8 19 0.31
9 8 0.13
10 3 0.05
ACGTcount: A:0.81, C:0.05, G:0.13, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:517596 original size:22 final size:22
Alignment explanation
Indices: 517568--517622 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
517558 GCTGTCCCAT
517568 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
517590 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
517612 CAAACCTTTGA
1 CAAACCTTTGA
517623 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:518058 original size:18 final size:18
Alignment explanation
Indices: 518035--518070 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
518025 TCAACATCAA
* *
518035 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
518053 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
518071 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:518539 original size:36 final size:35
Alignment explanation
Indices: 518499--518795 Score: 164
Period size: 36 Copynumber: 8.5 Consensus size: 35
518489 ACTCATGATT
* * *
518499 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * **
518535 GTTT-TCACTAGAAGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* * *
518570 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* *
518606 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * * * *
518642 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* *
518670 TGTTT-TCTTTGAAACAAATTTCGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATTT-GTCTCTCTTGAGACA
* ** *
518707 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * * *
518744 G-TTCTCTTGAATCAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
518779 GTTACTCTTGAAACAAA
1 GTTTCTCTTAAAACAAA
518796 AAATCTTCAA
Statistics
Matches: 206, Mismatches: 36, Indels: 38
0.74 0.13 0.14
Matches are distributed among these distances:
28 3 0.01
29 18 0.09
30 3 0.01
34 4 0.02
35 47 0.23
36 108 0.52
37 20 0.10
38 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:518647 original size:72 final size:72
Alignment explanation
Indices: 518555--518791 Score: 242
Period size: 72 Copynumber: 3.4 Consensus size: 72
518545 GAAGAGTTTT
*
518555 GTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 GTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
518620 AAATTTC
66 AAATTTC
* * * *
518627 GTCTATCTTGAGACAGTTTCCCTTGAAACAAA------ATAT-TTGA-ATATGTTT-TCTTTGAA
1 GTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA-GTTTCTC-TTGAA
518683 ACAAATTTC
64 ACAAATTTC
** ** * * *
518692 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG-TTCTCTTGAAT
1 GTCTATCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
*
518756 CAATTTTC
65 CAAATTTC
* *
518764 GTCTATCTTGAGACAGTTACTCTTGAAA
1 GTCTATCTTGAGACAGTTTCCCTTGAAA
518792 CAAAAAATCT
Statistics
Matches: 131, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
64 4 0.03
65 42 0.32
66 7 0.05
71 3 0.02
72 66 0.50
73 7 0.05
74 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (72 bp):
GTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAATTTC
Found at i:518739 original size:37 final size:36
Alignment explanation
Indices: 518673--518790 Score: 127
Period size: 35 Copynumber: 3.3 Consensus size: 36
518663 TTGAATATGT
* * *
518673 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAATCAATTTTCGTCTCTCTTGAGACAG
*
518708 TTTCTTTTGGAA-CTAAGTTTT-GTCTCTCTTGAGACAG
1 TTTCTCTT-GAATC-AA-TTTTCGTCTCTCTTGAGACAG
*
518745 -TTCTCTTGAATCAATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAATCAATTTTCGTCTCTCTTGAGACAG
*
518780 TTACTCTTGAA
1 TTTCTCTTGAA
518791 ACAAAAAATC
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
34 4 0.06
35 25 0.35
36 19 0.27
37 20 0.28
38 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAATCAATTTTCGTCTCTCTTGAGACAG
Found at i:519695 original size:105 final size:105
Alignment explanation
Indices: 519466--520126 Score: 956
Period size: 105 Copynumber: 6.3 Consensus size: 105
519456 GCCATCCGCG
* * * * * *
519466 ATTTCAACTCCACGACGGAGGATATCATGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
519531 GGGACGGCTAG-TTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCT-GCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
519575 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGC
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
519640 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
519680 ATTTCAACTTTACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
519745 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
519785 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
519850 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
519890 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
519955 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
519990 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
520055 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
520096 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
520127 TGGAACAATG
Statistics
Matches: 510, Mismatches: 35, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
100 82 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 308 0.60
106 82 0.16
107 3 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:520718 original size:34 final size:37
Alignment explanation
Indices: 520674--520775 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
520664 TTTCGTCCTA
520674 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
*
520709 -TAGGATTCAAACTCCTAAAAATATGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
520744 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
520776 GTTCTACTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
35 3 0.05
37 27 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:520759 original size:37 final size:35
Alignment explanation
Indices: 520674--520809 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
520664 TTTCGTCCTA
520674 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
520709 -TAGGATTCAAACTCCTAAAAATATGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
520744 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
520781 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
520810 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 28 0.32
35 3 0.03
36 2 0.02
37 52 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:521465 original size:2 final size:2
Alignment explanation
Indices: 521460--521488 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
521450 CTTATAACTT
521460 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 T
521489 TATTGCGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:522720 original size:12 final size:12
Alignment explanation
Indices: 522703--522727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
522693 AAAAAGTTTA
522703 GCAGTACTCTTT
1 GCAGTACTCTTT
522715 GCAGTACTCTTT
1 GCAGTACTCTTT
522727 G
1 G
522728 GTATAAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GCAGTACTCTTT
Found at i:534687 original size:172 final size:173
Alignment explanation
Indices: 534402--534749 Score: 673
Period size: 172 Copynumber: 2.0 Consensus size: 173
534392 TTGATCATCG
534402 TCATCACATAATGCTGAGATATATAACACAAACCTGAATAGAACAAGGAGAAAATTTATATTTTT
1 TCATCACATAATGCTGAGATATATAACACAAACCTGAATAGAACAAGGAGAAAATTTATATTTTT
534467 GCATTAAGCATATAGACTGGAATTACTCCATTCTAGGTATGCATAAGATCGG-AAAATTTAACCA
66 GCATTAAGCATATAGACTGGAATTACTCCATTCTAGGTATGCATAAGATCGGAAAAATTTAACCA
534531 AGTTACAAATAATGACAGTGAAG-TTCTCTATGCACTTCATTA
131 AGTTACAAATAATGACAGTGAAGTTTCTCTATGCACTTCATTA
534573 TCATCACATAATGCTGAGATATATAACACAAACCTGAATAGAACAAGGAGAAAATTTTATATTTT
1 TCATCACATAATGCTGAGATATATAACACAAACCTGAATAGAACAAGGAGAAAA-TTTATATTTT
534638 TGCATTAAGCATATAGACTGGAATTACTCCATTCTAGGTATGCATAAGATCGGAAAAATTTAACC
65 TGCATTAAGCATATAGACTGGAATTACTCCATTCTAGGTATGCATAAGATCGGAAAAATTTAACC
534703 AAGTTACAAATAATGACAGTGAAGTTTCTCTATGCACTTCATTA
130 AAGTTACAAATAATGACAGTGAAGTTTCTCTATGCACTTCATTA
534747 TCA
1 TCA
534750 AAAACTTAAA
Statistics
Matches: 174, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
171 54 0.31
172 63 0.36
173 35 0.20
174 22 0.13
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (173 bp):
TCATCACATAATGCTGAGATATATAACACAAACCTGAATAGAACAAGGAGAAAATTTATATTTTT
GCATTAAGCATATAGACTGGAATTACTCCATTCTAGGTATGCATAAGATCGGAAAAATTTAACCA
AGTTACAAATAATGACAGTGAAGTTTCTCTATGCACTTCATTA
Found at i:538499 original size:20 final size:20
Alignment explanation
Indices: 538474--538511 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
538464 ATTTACAAAT
538474 TTTAAAAA-AGGTAAAAAAAG
1 TTTAAAAATA-GTAAAAAAAG
538494 TTTAAAAATAGTAAAAAA
1 TTTAAAAATAGTAAAAAA
538512 TAACATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (20 bp):
TTTAAAAATAGTAAAAAAAG
Found at i:541003 original size:65 final size:65
Alignment explanation
Indices: 540792--541236 Score: 698
Period size: 65 Copynumber: 6.9 Consensus size: 65
540782 ATAAGTATAG
*
540792 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGATGGAGTGATAATTGAATAC-A-ACAT
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
* * * *
540855 ATCACTCATATGACTCATATACCTTTGTGGTGCATGGGGTCGAGTGATAATT-AATACAATGCAT
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
*
540919 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAA
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
* * *
540984 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAAGTGGAGTGATAATTGAATACAGTACAA
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
* *
541049 ATCACTCATATGACTCATGTACCTTTGTAGTGCATGAGGTGGAGTGATAATTGTATACAATACAT
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
* * * * * **
541114 ATCACCCATATGACTAATATACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATATAATATGT
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
*
541179 ATCATTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
1 ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
541237 TGCAAAGATC
Statistics
Matches: 347, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
62 5 0.01
63 49 0.14
64 52 0.15
65 241 0.69
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (65 bp):
ATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATACAT
Found at i:542543 original size:65 final size:65
Alignment explanation
Indices: 542079--542531 Score: 658
Period size: 65 Copynumber: 7.0 Consensus size: 65
542069 ACTAGACTTG
*
542079 AATACAGATCACTC--ATGACTCATGTACCTTTGTGGTGCATGAGATGGAGTGATAATTGAATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
* * * * *
542142 AATACATATCACTCATATGACTTATGTACCTTTGTGGTACATGGGGTCGAGTGATAATTGAATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
* * * * *
542207 AGTACAGATCACTCATATGACTCATGTATCTTTGTGGTGTATGAGGTGGAATGATAATTAAATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
* * **
542272 AATACAAATCACTCACATGACTCATGTACCTTTGTGGTGCATGAAATGGAGTGATAATTGAATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
* * * * *
542337 AATACATATCACTCATATGATTCATGTACCTTTATGGTGCATTAGGTGGAGTGATAATTGTATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
* * * *
542402 AATATAGATCACTCATATGACTAATATACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
* *
542467 AATACATATCACTCATATGATTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
1 AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
542532 TGCAAAGATC
Statistics
Matches: 341, Mismatches: 47, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
63 13 0.04
65 328 0.96
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (65 bp):
AATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAC
Found at i:546474 original size:33 final size:33
Alignment explanation
Indices: 546407--546494 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
546397 AAAGATGAAA
* * *
546407 AATAAGTTAGCCACCTACCAA-A-GATTTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
546438 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
546471 AATAAATTGGCCACCAACCAAGAT
1 AATAAGTTGGCCACCAACCAAGAT
546495 AAAATTTCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 19 0.37
32 1 0.02
33 31 0.61
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:546512 original size:29 final size:32
Alignment explanation
Indices: 546433--546502 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
546423 ACCAAAGATT
* * *
546433 TTTCCAATAAGTTGGCCACCAACCAAGATGAAT
1 TTTCC-ATAAATTGGCCACCAACCAAGATAAAA
546466 TTTCCAATAAATTGGCCACCAACCAAGATAAAA
1 TTTCC-ATAAATTGGCCACCAACCAAGATAAAA
546499 TTTC
1 TTTC
546503 TAACTTGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (32 bp):
TTTCCATAAATTGGCCACCAACCAAGATAAAA
Found at i:551133 original size:33 final size:31
Alignment explanation
Indices: 551065--551133 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
551055 AAAGATGAAA
** * * *
551065 AATAAGTTGGTCACCTACCAAAGATTTTTCT
1 AATAAGTTGACCACCAACCAAAGAATTTTCC
551096 AATAAGTTGACCACCAACCAAGATGAATTTTCC
1 AATAAGTTGACCACCAACCAA-A-GAATTTTCC
551129 AATAA
1 AATAA
551134 ATTGGATACC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 18 0.58
32 1 0.03
33 12 0.39
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (31 bp):
AATAAGTTGACCACCAACCAAAGAATTTTCC
Found at i:553537 original size:20 final size:21
Alignment explanation
Indices: 553512--553555 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
553502 GTGAATATGA
553512 AAAAGTTA-AAACTCTTCTAT
1 AAAAGTTAGAAACTCTTCTAT
*
553532 AAAAGTTAGGAACTCTTCTAT
1 AAAAGTTAGAAACTCTTCTAT
553553 AAA
1 AAA
553556 CATTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (21 bp):
AAAAGTTAGAAACTCTTCTAT
Found at i:558588 original size:3 final size:3
Alignment explanation
Indices: 558582--558612 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
558572 TTTTTATTTC
558582 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
558613 TATAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:566011 original size:34 final size:36
Alignment explanation
Indices: 565934--566060 Score: 156
Period size: 34 Copynumber: 3.6 Consensus size: 36
565924 ACAAAGTGTC
*
565934 GTCTCGCTAGAGACAATTTT-TCTTAAAAACAAATTTT
1 GTCTCGCTTGAGACAATTTTCTCTT-AAAACAAA-TTT
*
565971 GTCTCGCTTGAGATAATTTTCTC-TAAAA-AAATTT
1 GTCTCGCTTGAGACAATTTTCTCTTAAAACAAATTT
566005 GTCTCGCTTGAGACAA-TTTCTCTTAAAACAAATTT
1 GTCTCGCTTGAGACAATTTTCTCTTAAAACAAATTT
* *
566040 CATCTCCCTTGAGA-AATTTTC
1 -GTCTCGCTTGAGACAATTTTC
566061 CCTCGGAACA
Statistics
Matches: 80, Mismatches: 5, Indels: 11
0.83 0.05 0.11
Matches are distributed among these distances:
33 6 0.08
34 23 0.29
35 11 0.14
36 19 0.24
37 19 0.24
38 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTTCTCTTAAAACAAATTT
Found at i:566276 original size:36 final size:37
Alignment explanation
Indices: 566222--566344 Score: 153
Period size: 36 Copynumber: 3.4 Consensus size: 37
566212 CTTTGAGATT
* * *
566222 GTTTTCCTTGGAAC-AAGTTTTGTCTCCCTTAAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
* *
566258 GTTTCCCTTTAAA-AAAGTTTTGCCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
** *
566294 GTTTCCCAGGAAACAAAGTTTT-TCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
566330 GTTTCCCTTGAAACA
1 GTTTCCCTTGAAACA
566345 CAAACATTGA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
36 65 0.89
37 8 0.11
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (37 bp):
GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
Found at i:567198 original size:23 final size:23
Alignment explanation
Indices: 567170--567221 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
567160 CCCAACCCGA
567170 CCCAAAGTCTGACCCGTTTCAGG
1 CCCAAAGTCTGACCCGTTTCAGG
567193 CCCAAAGTCTGACCCGTTTCAGG
1 CCCAAAGTCTGACCCGTTTCAGG
567216 CCCAAA
1 CCCAAA
567222 TTAAGTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.37, G:0.19, T:0.19
Consensus pattern (23 bp):
CCCAAAGTCTGACCCGTTTCAGG
Found at i:567309 original size:17 final size:17
Alignment explanation
Indices: 567269--567309 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
567259 CAGACCCGGA
*
567269 TGACCCAATTCAAGCCG
1 TGACCCGATTCAAGCCG
*
567286 TGACCCGATTCAAGCGG
1 TGACCCGATTCAAGCCG
567303 TGACCCG
1 TGACCCG
567310 TGTCCAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.17
Consensus pattern (17 bp):
TGACCCGATTCAAGCCG
Found at i:575396 original size:2 final size:2
Alignment explanation
Indices: 575354--575380 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
575344 CTTATATTTA
575354 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
575381 AATTTAAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:580594 original size:16 final size:15
Alignment explanation
Indices: 580575--580617 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
580565 TTTTTGAATG
580575 TTTCTATTTTTTCTTC
1 TTTCT-TTTTTTCTTC
580591 TTTCTTCTTTTTC-TC
1 TTTCTT-TTTTTCTTC
580606 TTT-TTTTTTTCT
1 TTTCTTTTTTTCT
580618 GCTTGAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.24
14 2 0.08
15 6 0.24
16 11 0.44
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTTCTTC
Found at i:583575 original size:30 final size:28
Alignment explanation
Indices: 583541--583604 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
583531 TCCTTCTTTT
583541 TTCTTTTGGA-TTATGCACCAACTTCACTTC
1 TTCTTTTGGAGTT-TGCACCAA-TT-ACTTC
**
583571 TTCTTTTGGAGTTTGCGTCAATTACTTC
1 TTCTTTTGGAGTTTGCACCAATTACTTC
583599 TTCTTT
1 TTCTTT
583605 CATATGGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 11 0.35
29 2 0.06
30 16 0.52
31 2 0.06
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (28 bp):
TTCTTTTGGAGTTTGCACCAATTACTTC
Found at i:587016 original size:18 final size:17
Alignment explanation
Indices: 586993--587026 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
586983 CCGCTACTAG
586993 TGAACCGGTCGAAACCGT
1 TGAACCGGTC-AAACCGT
*
587011 TGAACCGTTCAAACCG
1 TGAACCGGTCAAACCG
587027 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (17 bp):
TGAACCGGTCAAACCGT
Found at i:588304 original size:71 final size:74
Alignment explanation
Indices: 588216--588360 Score: 260
Period size: 71 Copynumber: 2.0 Consensus size: 74
588206 TGGCAACCAA
588216 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTT-AAAAATGG-TTTTCAAAGTTTGG
1 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTTCAAAGTTTGG
588279 TAAATGTTT
66 TAAATGTTT
588288 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTTCAAAGTTTGG
1 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTTCAAAGTTTGG
*
588352 TAGATGTTT
66 TAAATGTTT
588361 GTTGAAATAT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
71 35 0.50
72 13 0.19
73 22 0.31
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (74 bp):
CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTTTTCAAAGTTTGG
TAAATGTTT
Found at i:588367 original size:36 final size:36
Alignment explanation
Indices: 588216--588360 Score: 256
Period size: 36 Copynumber: 4.0 Consensus size: 36
588206 TGGCAACCAA
588216 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
588253 CTTT-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
588288 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
588324 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
588361 GTTGAAATAT
Statistics
Matches: 105, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
35 35 0.33
36 44 0.42
37 26 0.25
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:592751 original size:36 final size:38
Alignment explanation
Indices: 592698--592771 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
592688 TGGCAACAAA
592698 CTTTGAAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
592735 CTTTG-AAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
592772 GTTGAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 8 0.23
37 27 0.77
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (38 bp):
CTTTGAAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:599369 original size:40 final size:42
Alignment explanation
Indices: 599323--599459 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 42
599313 TTTTTCCAAA
* **
599323 AAACGCCGTAATAGAGAAG-AATTTTGCAGCGTTT-TACGGC
1 AAACGCCGTAATAGAGAAGTAATTTAGCAGCGTTTATACCAC
* * ** *
599363 AAACGCCGCAATATAGTGGTAATTTAGCGGCGTTTATACCAC
1 AAACGCCGTAATAGAGAAGTAATTTAGCAGCGTTTATACCAC
* * * * * *
599405 AAACGCCGTAATAGA-ATGATAAATTAGCGGCATTTATATCTC
1 AAACGCCGTAATAGAGAAG-TAATTTAGCAGCGTTTATACCAC
599447 AAACGCCGTAATA
1 AAACGCCGTAATA
599460 AATAATGCTT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 15 0.19
41 14 0.18
42 49 0.63
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (42 bp):
AAACGCCGTAATAGAGAAGTAATTTAGCAGCGTTTATACCAC
Found at i:599432 original size:42 final size:42
Alignment explanation
Indices: 599362--599459 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
599352 CGTTTTACGG
* * * * * *
599362 CAAACGCCGCAATATAGTGGTAATTTAGCGGCGTTTATACCA
1 CAAACGCCGTAATAGAATGATAAATTAGCGGCATTTATACCA
* *
599404 CAAACGCCGTAATAGAATGATAAATTAGCGGCATTTATATCT
1 CAAACGCCGTAATAGAATGATAAATTAGCGGCATTTATACCA
599446 CAAACGCCGTAATA
1 CAAACGCCGTAATA
599460 AATAATGCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (42 bp):
CAAACGCCGTAATAGAATGATAAATTAGCGGCATTTATACCA
Found at i:602715 original size:12 final size:12
Alignment explanation
Indices: 602698--602723 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
602688 TTTGCAAATG
602698 TTGACAAATGAT
1 TTGACAAATGAT
602710 TTGACAAATGAT
1 TTGACAAATGAT
602722 TT
1 TT
602724 AATGCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (12 bp):
TTGACAAATGAT
Found at i:603207 original size:20 final size:19
Alignment explanation
Indices: 603164--603210 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
603154 GATCTTAAGT
*
603164 TTAAAAAACTATATTTATAA
1 TTAAAAAA-TATATTAATAA
603184 --AAAAAATATTATTAATAA
1 TTAAAAAATA-TATTAATAA
603202 TTAAAAAAT
1 TTAAAAAAT
603211 TATAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.09
18 14 0.61
20 7 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAAATATATTAATAA
Found at i:609852 original size:43 final size:43
Alignment explanation
Indices: 609750--609852 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
609740 ATTATGTGTT
* *
609750 ATTTAACGGCGTTTGTA-ACAAAAACGCCGTAATATACCATAC
1 ATTTAGCGGCGTTTGTATACAAAAACGCCCTAATATACCATAC
* *
609792 ATTTAGCGGCGTTTGTATCATAAAAACGCCACT-ATATACCA-AT
1 ATTTAGCGGCGTTTGTAT-ACAAAAACGCC-CTAATATACCATAC
*
609835 TTTTAGCGGCGTTTGTAT
1 ATTTAGCGGCGTTTGTAT
609853 TAAAAATGCC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 16 0.30
43 18 0.34
44 18 0.34
45 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTATACAAAAACGCCCTAATATACCATAC
Found at i:610014 original size:43 final size:43
Alignment explanation
Indices: 609853--610014 Score: 207
Period size: 43 Copynumber: 3.8 Consensus size: 43
609843 GCGTTTGTAT
* * * * **
609853 TAAAAATGCCGCTAAACCTCAACGCCTATTGCGGCGTTTTAGC
1 TAAAAACGCCGCTAAATCTCAACACATATTGCAACGTTTTAGC
* * *
609896 TAAAAGCGTCGCTAAATCTCAACACATATTGCGACGTTTTAGC
1 TAAAAACGCCGCTAAATCTCAACACATATTGCAACGTTTTAGC
* *
609939 TAAAAACGTCGCTAAATCTCAACACATATTGCAACGTTTTCGC
1 TAAAAACGCCGCTAAATCTCAACACATATTGCAACGTTTTAGC
* *
609982 TAAAAATGCCGCTAAATCTCAAGACATATTGCA
1 TAAAAACGCCGCTAAATCTCAACACATATTGCA
610015 GCATTTGTGA
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
TAAAAACGCCGCTAAATCTCAACACATATTGCAACGTTTTAGC
Found at i:610036 original size:43 final size:43
Alignment explanation
Indices: 609905--610084 Score: 147
Period size: 43 Copynumber: 4.2 Consensus size: 43
609895 CTAAAAGCGT
* * *
609905 CGCTAAATCTCAACACATATTGC-GACGTTT-TAGCTA-AAAACGT
1 CGCTAAATCTCAAAACATATTGCAG-CGTTTGT-G-AAGAAAACGC
* * * *
609948 CGCTAAATCTCAACACATATTGCAACGTTT-TCGCTA-AAAATGC
1 CGCTAAATCTCAAAACATATTGCAGCGTTTGT-G-AAGAAAACGC
* *
609991 CGCTAAATCTCAAGACATATTGCAGCATTTGTGAAGAAAACGC
1 CGCTAAATCTCAAAACATATTGCAGCGTTTGTGAAGAAAACGC
* * *
610034 CGCTAAA-CATCAAAACCTACTGCGGCGTTTGTGAAGAAAACGC
1 CGCTAAATC-TCAAAACATATTGCAGCGTTTGTGAAGAAAACGC
*
610077 CACTAAAT
1 CGCTAAAT
610085 ATTAACAACT
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.02
43 114 0.97
44 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (43 bp):
CGCTAAATCTCAAAACATATTGCAGCGTTTGTGAAGAAAACGC
Found at i:610063 original size:86 final size:85
Alignment explanation
Indices: 609854--610063 Score: 210
Period size: 86 Copynumber: 2.4 Consensus size: 85
609844 CGTTTGTATT
* * * *
609854 AAAAATGCCGCTAAACCTCAACGCCTATTGCGGCGTTTTAGCTAAAAGCGTCGCTAAATCTCAAC
1 AAAAACGCCGCTAAA-CTCAACACCTATTGCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAAC
* *
609919 ACATATTGCGACGTTTTAGCT
65 ACATATTGCGACATTTTAGCA
* * ** * * *
609940 AAAAACGTCGCTAAATCTCAACACATATTGCAACGTTTTCGCTAAAAATGCCGCTAAATCTCAAG
1 AAAAACGCCGCTAAA-CTCAACACCTATTGCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAAC
610005 ACATATTGC-AGCATTTGT-G-A
65 ACATATTGCGA-CATTT-TAGCA
* *
610025 AGAAAACGCCGCTAAACATCAAAACCTACTGCGGCGTTT
1 A-AAAACGCCGCTAAAC-TCAACACCTATTGCGGCGTTT
610064 GTGAAGAAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
85 3 0.03
86 96 0.96
87 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (85 bp):
AAAAACGCCGCTAAACTCAACACCTATTGCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACA
CATATTGCGACATTTTAGCA
Found at i:611442 original size:43 final size:43
Alignment explanation
Indices: 611385--611467 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
611375 TGAAATTTCC
611385 CCATCCACTGTTCAACAATTGCCAGCTTGAATTCGATGCATTT
1 CCATCCACTGTTCAACAATTGCCAGCTTGAATTCGATGCATTT
* * *
611428 CCATCCACAT-TTCAATAATTGTCAGCTTGAATTCGGTGCA
1 CCATCCAC-TGTTCAACAATTGCCAGCTTGAATTCGATGCA
611468 ATAAATGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (43 bp):
CCATCCACTGTTCAACAATTGCCAGCTTGAATTCGATGCATTT
Found at i:616108 original size:20 final size:21
Alignment explanation
Indices: 616083--616124 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
616073 TATCGGTGAC
616083 TGGAAATTACTGCTAA-TGAT
1 TGGAAATTACTGCTAATTGAT
*
616103 TGGAAATTAGTGCTAATTGAT
1 TGGAAATTACTGCTAATTGAT
616124 T
1 T
616125 TAGGGATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (21 bp):
TGGAAATTACTGCTAATTGAT
Found at i:627330 original size:34 final size:35
Alignment explanation
Indices: 627263--627329 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
627253 TTAAGTTTGG
* *
627263 TTCTAGAAAAAATTTTTATGTTTTTGTTTTTTTAT
1 TTCTAGAAAAAATTTTCATGTTTTAGTTTTTTTAT
627298 TTCTAGAAAATAATTTTCAT-TTTTAGTTTTTT
1 TTCTAGAAAA-AATTTTCATGTTTTAGTTTTTT
627330 AAAAATTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 21 0.72
36 8 0.28
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.61
Consensus pattern (35 bp):
TTCTAGAAAAAATTTTCATGTTTTAGTTTTTTTAT
Found at i:627386 original size:5 final size:6
Alignment explanation
Indices: 627370--627394 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
627360 AATGAAAACT
627370 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
627395 GGTCAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:627734 original size:29 final size:29
Alignment explanation
Indices: 627699--627754 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
627689 GTAAATGAGT
* **
627699 TTAATTAATTTTTTATTAAGTTTGAGGGC
1 TTAATTAATATTTTAGAAAGTTTGAGGGC
627728 TTAATTAATATTTTAGAAAGTTTGAGG
1 TTAATTAATATTTTAGAAAGTTTGAGG
627755 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (29 bp):
TTAATTAATATTTTAGAAAGTTTGAGGGC
Found at i:629852 original size:12 final size:12
Alignment explanation
Indices: 629835--629859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
629825 AATTGCGAAG
629835 ATTAAAATTTAA
1 ATTAAAATTTAA
629847 ATTAAAATTTAA
1 ATTAAAATTTAA
629859 A
1 A
629860 AACCCGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAAATTTAA
Found at i:630094 original size:10 final size:10
Alignment explanation
Indices: 630035--630093 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
630025 GAAAAAGGAA
630035 AAAAATAAAT
1 AAAAATAAAT
*
630045 AAAAATAGAT
1 AAAAATAAAT
*
630055 CAAAAAGAAA-
1 -AAAAATAAAT
*
630065 AAAATTAAAT
1 AAAAATAAAT
*
630075 AAATATAAA-
1 AAAAATAAAT
630084 AATAAATAAA
1 AA-AAATAAA
630094 AGAATATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
9 9 0.24
10 22 0.58
11 7 0.18
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:630149 original size:28 final size:26
Alignment explanation
Indices: 630116--630213 Score: 80
Period size: 28 Copynumber: 3.8 Consensus size: 26
630106 TAACAATAAT
* *
630116 AAAAAATAAAGATAAGTGAAATTAAGAA
1 AAAAAATAAAAATAA--GAAAATAAGAA
630144 AAAAAATAAAAATAAGAAAATAAGAA
1 AAAAAATAAAAATAAGAAAATAAGAA
630170 AATAAAA-AGCAAAAT-AG-AAAT-AGAA
1 AA-AAAATA--AAAATAAGAAAATAAGAA
* *
630195 AAAATA-AAAAATAAAAAAA
1 AAAAAATAAAAATAAGAAAA
630214 GGTTATATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
22 5 0.08
23 1 0.02
24 7 0.11
25 6 0.10
26 17 0.28
27 6 0.10
28 19 0.31
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.13
Consensus pattern (26 bp):
AAAAAATAAAAATAAGAAAATAAGAA
Found at i:630154 original size:8 final size:8
Alignment explanation
Indices: 630142--630213 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
630132 TGAAATTAAG
630142 AAAAAAA-
1 AAAAAAAT
*
630149 ATAAAAAT
1 AAAAAAAT
*
630157 AAGAAAAT
1 AAAAAAAT
*
630165 AAGAAAAT
1 AAAAAAAT
630173 AAAAAGCAA-
1 AAAAA--AAT
*
630182 AATAGAAAT
1 AA-AAAAAT
630191 AGAAAAAAT
1 A-AAAAAAT
630200 -AAAAAAT
1 AAAAAAAT
630207 AAAAAAA
1 AAAAAAA
630214 GGTTATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
7 13 0.25
8 26 0.50
9 8 0.15
10 5 0.10
ACGTcount: A:0.81, C:0.01, G:0.07, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:630184 original size:34 final size:34
Alignment explanation
Indices: 630146--630211 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
630136 ATTAAGAAAA
*
630146 AAAATAAAAATA-AGAAAATAAGAAAATAAAAAGC
1 AAAATAAAAATAGAAAAAATAA-AAAATAAAAAGC
*
630180 AAAATAGAAATAGAAAAAATAAAAAATAAAAA
1 AAAATAAAAATAGAAAAAATAAAAAATAAAAA
630212 AAGGTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.12
Consensus pattern (34 bp):
AAAATAAAAATAGAAAAAATAAAAAATAAAAAGC
Found at i:630188 original size:27 final size:28
Alignment explanation
Indices: 630152--630204 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
630142 AAAAAAAATA
*
630152 AAAATAAGAAAATA-AGAAAATAAAAAGC
1 AAAATAAG-AAATAGAAAAAATAAAAAGC
630180 AAAAT-AGAAATAGAAAAAATAAAAA
1 AAAATAAGAAATAGAAAAAATAAAAA
630205 ATAAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 13 0.57
28 5 0.22
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (28 bp):
AAAATAAGAAATAGAAAAAATAAAAAGC
Found at i:632160 original size:16 final size:16
Alignment explanation
Indices: 632139--632173 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
632129 TCAAAGTGTA
632139 AATAATATAAAAATTC
1 AATAATATAAAAATTC
*
632155 AATAATCTAAAAATTC
1 AATAATATAAAAATTC
632171 AAT
1 AAT
632174 GATCATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATATAAAAATTC
Found at i:635321 original size:21 final size:21
Alignment explanation
Indices: 635295--635339 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
635285 GATTTCTGGG
* *
635295 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
635316 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
635337 CAA
1 CAA
635340 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Done.