Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 21
Found at i:403119 original size:14 final size:14
Alignment explanation
Indices: 403102--403188 Score: 52
Period size: 14 Copynumber: 6.0 Consensus size: 14
403092 TTTAGTAATT
403102 ATTATTAATAATGA
1 ATTATTAATAATGA
*
403116 ATTATTATTAAT-A
1 ATTATTAATAATGA
* * *
403129 TTTAATTATTTGATATTA
1 ATT-ATTA-AT-A-ATGA
*
403147 ATGATTAAGTAATG-
1 ATTATTAA-TAATGA
*
403161 ATTAGTAATAATGA
1 ATTATTAATAATGA
*
403175 AATATTAATAATGA
1 ATTATTAATAATGA
403189 TTTAATCATT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
13 8 0.14
14 33 0.59
15 4 0.07
16 2 0.04
17 7 0.12
18 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
ATTATTAATAATGA
Found at i:403120 original size:17 final size:17
Alignment explanation
Indices: 403098--403138 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
403088 ATGATTTAGT
403098 AATTATTATTAATAATG
1 AATTATTATTAATAATG
* *
403115 AATTATTATTAATATTT
1 AATTATTATTAATAATG
403132 AATTATT
1 AATTATT
403139 TGATATTAAT
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:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTATTATTAATAATG
Found at i:403133 original size:24 final size:25
Alignment explanation
Indices: 403075--403134 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
403065 ATAATGATAG
*
403075 TAATGATTTAATAATGATTTAGTAAT
1 TAAT-ATTTAATAATGAATTAGTAAT
* *
403101 TATTA-TTAATAATGAATTA-TTAT
1 TAATATTTAATAATGAATTAGTAAT
403124 TAATATTTAAT
1 TAATATTTAAT
403135 TATTTGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 7 0.24
24 18 0.62
25 1 0.03
26 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (25 bp):
TAATATTTAATAATGAATTAGTAAT
Found at i:403201 original size:18 final size:18
Alignment explanation
Indices: 403178--403230 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
403168 ATAATGAAAT
403178 ATTAATAATGATTTAATC
1 ATTAATAATGATTTAATC
403196 ATTAATAATGATTTAATC
1 ATTAATAATGATTTAATC
*
403214 TTTAATAATGATTTAAT
1 ATTAATAATGATTTAAT
403231 TTCTAACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (18 bp):
ATTAATAATGATTTAATC
Found at i:403202 original size:24 final size:24
Alignment explanation
Indices: 403082--403202 Score: 97
Period size: 24 Copynumber: 5.0 Consensus size: 24
403072 TAGTAATGAT
* *
403082 TTAATAATGATTTAGTAATTATTA
1 TTAATAATGATTTAATAATTAATA
* *
403106 TTAATAATGAATT-ATTATTAATA
1 TTAATAATGATTTAATAATTAATA
* *
403129 TT--TAATTATTTGAT-ATTAATGA
1 TTAATAATGATTTAATAATTAAT-A
*
403151 TTAAGTAATGATTAGTAATAATGAAATA
1 TTAA-TAATGATT--TAATAAT-TAATA
*
403179 TTAATAATGATTTAATCATTAATA
1 TTAATAATGATTTAATAATTAATA
403203 ATGATTTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
21 13 0.17
22 5 0.06
23 9 0.12
24 16 0.21
25 13 0.17
27 11 0.14
28 7 0.09
29 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (24 bp):
TTAATAATGATTTAATAATTAATA
Found at i:403230 original size:11 final size:11
Alignment explanation
Indices: 402989--403194 Score: 80
Period size: 11 Copynumber: 17.1 Consensus size: 11
402979 TTTCATGATT
*
402989 TAATGATTTAG
1 TAATGATTTAA
403000 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
403014 TAATCATTATAA
1 TAATGATT-TAA
403026 TAATGATTTAGTAA
1 TAATGA-TT--TAA
*
403040 TAATCATTATAA
1 TAATGATT-TAA
*
403052 TAATGATTTGA
1 TAATGATTTAA
* * *
403063 TAATAATGATAG
1 TAATGAT-TTAA
403075 TAATGATTTAA
1 TAATGATTTAA
*
403086 TAATGATTTAG
1 TAATGATTTAA
*
403097 TAATTATTATTAA
1 TAATGA-T-TTAA
*
403110 TAATGAATTATTAT
1 TAATG-A-T-TTAA
403124 TAAT-ATTTAA
1 TAATGATTTAA
403134 T--T-ATTTGATA
1 TAATGATTT-A-A
403144 TTAATGA-TTAA
1 -TAATGATTTAA
403155 GTAATGATTAGTAA
1 -TAATGATT--TAA
403169 TAATGAAATATTAA
1 TAATG--AT-TTAA
403183 TAATGATTTAA
1 TAATGATTTAA
403194 T
1 T
403195 CATTAATAAT
Statistics
Matches: 152, Mismatches: 22, Indels: 42
0.70 0.10 0.19
Matches are distributed among these distances:
8 5 0.03
9 1 0.01
10 5 0.03
11 45 0.30
12 34 0.22
13 21 0.14
14 38 0.25
15 2 0.01
16 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:403546 original size:23 final size:26
Alignment explanation
Indices: 403518--403610 Score: 138
Period size: 26 Copynumber: 3.7 Consensus size: 26
403508 TTTGATGATT
* *
403518 TAATAATGATTTGATAATAATCATTA
1 TAATAATGATTTAATAATAATCAGTA
*
403544 TAATAATGATTTAGTAATAATCAGTA
1 TAATAATGATTTAATAATAATCAGTA
403570 TAATAATGATTTAATAATAAT--G-A
1 TAATAATGATTTAATAATAATCAGTA
403593 TAATAATGATTTAATAAT
1 TAATAATGATTTAATAAT
403611 GATTTAGTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
23 19 0.30
24 1 0.02
26 43 0.68
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (26 bp):
TAATAATGATTTAATAATAATCAGTA
Found at i:403547 original size:26 final size:25
Alignment explanation
Indices: 403518--403631 Score: 121
Period size: 26 Copynumber: 4.6 Consensus size: 25
403508 TTTGATGATT
403518 TAATAATGATTTGATAATAATCATTA
1 TAATAATGATTT-ATAATAATCATTA
*
403544 TAATAATGATTTAGTAATAATCAGTA
1 TAATAATGATTTA-TAATAATCATTA
* *
403570 TAATAATGA-TT-TAATAATAATGA
1 TAATAATGATTTATAATAATCATTA
*
403593 TAATAATGA-TT-TAATAATGATT-
1 TAATAATGATTTATAATAATCATTA
*
403615 TAGTAATGATTTGATAA
1 TAATAATGATTT-ATAA
403632 AAATGATTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
22 8 0.10
23 31 0.40
25 6 0.08
26 32 0.42
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (25 bp):
TAATAATGATTTATAATAATCATTA
Found at i:403586 original size:11 final size:11
Alignment explanation
Indices: 403452--403631 Score: 99
Period size: 11 Copynumber: 15.1 Consensus size: 11
403442 TAATAATTAT
*
403452 ATGATTTAGTA
1 ATGATTTAATA
403463 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
403477 ACGATTTAATA
1 ATGATTTAATA
403488 ATGATTTTAATA
1 ATGA-TTTAATA
* * * * * *
403500 GTTAATGATTTG
1 ATGATTTA-ATA
403512 ATGATTTAATA
1 ATGATTTAATA
403523 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
403537 ATCATTATAATA
1 ATGATT-TAATA
403549 ATGATTTAGTAATA
1 ATGA-TT--TAATA
* *
403563 ATCAGTATAATA
1 ATGA-TTTAATA
403575 ATGATTTAATA
1 ATGATTTAATA
* *
403586 ATAATGATAATA
1 ATGAT-TTAATA
403598 ATGATTTAATA
1 ATGATTTAATA
*
403609 ATGATTTAGTA
1 ATGATTTAATA
*
403620 ATGATTTGATA
1 ATGATTTAATA
403631 A
1 A
403632 AAATGATTTA
Statistics
Matches: 128, Mismatches: 30, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
11 54 0.42
12 44 0.34
13 6 0.05
14 24 0.19
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:403711 original size:14 final size:13
Alignment explanation
Indices: 403518--403702 Score: 107
Period size: 14 Copynumber: 14.9 Consensus size: 13
403508 TTTGATGATT
403518 TAATAATGATTTGA
1 TAATAATGATTT-A
*
403532 TAATAATCA-TTA
1 TAATAATGATTTA
403544 TAATAATGATTTA
1 TAATAATGATTTA
* *
403557 GTAATAATCA-GTA
1 -TAATAATGATTTA
403570 TAATAATGATTTAA
1 TAATAATGATTT-A
403584 TAATAATG----A
1 TAATAATGATTTA
403593 TAATAATGA-TT-
1 TAATAATGATTTA
403604 TAATAATGA-TT-
1 TAATAATGATTTA
*
403615 TAGTAATGATTTGA
1 TAATAATGATTT-A
*
403629 TAAAAATGATTTA
1 TAATAATGATTTA
*
403642 TTATTAAT-A--T-
1 -TAATAATGATTTA
403652 T--TAATGATTTGA
1 TAATAATGATTT-A
*
403664 TACTAATGA-TTA
1 TAATAATGATTTA
*
403676 CTAATAATGAAATTA
1 -TAATAATG-ATTTA
403691 TAATAATGATTT
1 TAATAATGATTT
403703 GATACTAATA
Statistics
Matches: 137, Mismatches: 13, Indels: 43
0.71 0.07 0.22
Matches are distributed among these distances:
7 4 0.03
8 1 0.01
9 10 0.07
10 1 0.01
11 20 0.15
12 21 0.15
13 22 0.16
14 55 0.40
15 3 0.02
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (13 bp):
TAATAATGATTTA
Found at i:406287 original size:44 final size:46
Alignment explanation
Indices: 406214--406302 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 46
406204 ACTAATTAAC
* *
406214 TATTTTTTATATATAACTAACGACTAACAAACAAATTAATTAATTAT
1 TATTTTTAATATATAACTAACGAC-AACAAACAAATTAAATAATTAT
* *
406261 TATTTTTAATATATAACTATC-A-AACAAACTAATTAAATAATT
1 TATTTTTAATATATAACTAACGACAACAAACAAATTAAATAATT
406303 TTTTATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 18 0.47
46 1 0.03
47 19 0.50
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.40
Consensus pattern (46 bp):
TATTTTTAATATATAACTAACGACAACAAACAAATTAAATAATTAT
Found at i:407353 original size:19 final size:19
Alignment explanation
Indices: 407329--407380 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
407319 TTTATGTCTG
407329 TTAATATGTAAATAAAATA
1 TTAATATGTAAATAAAATA
407348 TTAATATGTAAATAAAATA
1 TTAATATGTAAATAAAATA
407367 TTAATATGTAAATA
1 TTAATATGTAAATA
407381 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (19 bp):
TTAATATGTAAATAAAATA
Found at i:409573 original size:40 final size:40
Alignment explanation
Indices: 409512--409740 Score: 144
Period size: 40 Copynumber: 5.7 Consensus size: 40
409502 GTACTATAGC
* *
409512 GGCGTTTTTATAAAAATGCCGCTAAATAATGTTCTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAATAATGTTCTTTAGT
* * ** *
409552 GGCGTTTTTATACAAACGCCGCTAAA-GA-CTAATTTATT
1 GGCGTTTTTATACAAACGCCGCTAAATAATGTTCTTTAGT
* * * * **
409590 GGCATTTTTGTACAAACGCAGCTATAGTACGA-G-TCTTTACC
1 GGCGTTTTTATACAAACGCCGCTA-AATA--ATGTTCTTTAGT
* * * * * * * *
409631 GGTGTTTTTTATATAAACGCCGCTATAGACTCATTCTATAGC
1 GGCG-TTTTTATACAAACGCCGCTAAATAAT-GTTCTTTAGT
* *
409673 GGCGTTTTTACAGAAACGCCGCTAAATAAT-TTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTAAATAATGTT-CTTTAGT
* *
409713 GGAGTTTTTATACAAACGCCGCGAAATA
1 GGCGTTTTTATACAAACGCCGCTAAATA
409741 TCAACACCTA
Statistics
Matches: 139, Mismatches: 41, Indels: 18
0.70 0.21 0.09
Matches are distributed among these distances:
38 27 0.19
39 4 0.03
40 53 0.38
41 28 0.20
42 27 0.19
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (40 bp):
GGCGTTTTTATACAAACGCCGCTAAATAATGTTCTTTAGT
Found at i:409733 original size:81 final size:80
Alignment explanation
Indices: 409482--409734 Score: 244
Period size: 81 Copynumber: 3.1 Consensus size: 80
409472 CATTTCTAGA
* * * *
409482 ACAAACGCCGGTAAAGACTCGTACTATAGCGGCGTTTTTATAAAAATGCCGCTAAATAATGTTCT
1 ACAAACGCCGCTAAAGACTCATTCTATAGCGGCGTTTTTATAAAAACGCCGCTAAATAAT-TTCT
*
409547 TTAGTGGCGTTTTTAT
65 TTAGTGGAGTTTTTAT
* * * * * * * *
409563 ACAAACGCCGCTAAAGACTAATT-TAT--TGGCATTTTTGTACAAACGCAGCTATAGTACGA-GT
1 ACAAACGCCGCTAAAGACTCATTCTATAGCGGCGTTTTTATAAAAACGCCGCTA-AATA--ATTT
** *
409624 CTTTACCGGTGTTTTTTAT
63 CTTTAGTGGAG-TTTTTAT
* * * *
409643 ATAAACGCCGCTATAGACTCATTCTATAGCGGCGTTTTTACAGAAACGCCGCTAAATAATTTACT
1 ACAAACGCCGCTAAAGACTCATTCTATAGCGGCGTTTTTATAAAAACGCCGCTAAATAATTT-CT
409708 TTAGTGGAGTTTTTAT
65 TTAGTGGAGTTTTTAT
409724 ACAAACGCCGC
1 ACAAACGCCGC
409735 GAAATATCAA
Statistics
Matches: 133, Mismatches: 30, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
78 19 0.14
79 12 0.09
80 31 0.23
81 41 0.31
82 11 0.08
83 19 0.14
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (80 bp):
ACAAACGCCGCTAAAGACTCATTCTATAGCGGCGTTTTTATAAAAACGCCGCTAAATAATTTCTT
TAGTGGAGTTTTTAT
Found at i:409791 original size:43 final size:43
Alignment explanation
Indices: 409724--409908 Score: 253
Period size: 43 Copynumber: 4.3 Consensus size: 43
409714 GAGTTTTTAT
* *
409724 ACAAACGCCGCGAAATATCAACACCTATTGCGGTGTTTGTTGG
1 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG
* *
409767 AAAAAAGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG
1 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG
*
409810 ACAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTTGG
1 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG
* *** * *
409853 ACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTTTTTGTT
1 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTG-G
409897 ACCAAACGCCGC
1 A-CAAACGCCGC
409909 GAACTTTAGT
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
43 115 0.91
44 1 0.01
45 10 0.08
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGG
Found at i:410951 original size:91 final size:92
Alignment explanation
Indices: 410816--410990 Score: 244
Period size: 91 Copynumber: 1.9 Consensus size: 92
410806 GTTTTGTTCG
* * *
410816 ACAAACGCCATAATAGATATGTATAACATCATTTTTAGCGGCG-TTTTTGATCAAACACCATAAA
1 ACAAACGCCATAATAGAGATGTATAACATCATTTTTAGCAGCGTTTTTTGATCAAACACCACAAA
*
410880 ATACTCTTACTTTAGTGGCATTTTTTA
66 ATACTCTTACTTTAATGGCATTTTTTA
* * * * * **
410907 ACAAACGCCGTAATAGAGATGTATATCGTTATTTTTAGCAGCGTTTTTTTATCAAACGTCACAAA
1 ACAAACGCCATAATAGAGATGTATAACATCATTTTTAGCAGCGTTTTTTGATCAAACACCACAAA
410972 ATACTCTTACTTTAATGGC
66 ATACTCTTACTTTAATGGC
410991 GTTTGTATAC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
91 37 0.51
92 35 0.49
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (92 bp):
ACAAACGCCATAATAGAGATGTATAACATCATTTTTAGCAGCGTTTTTTGATCAAACACCACAAA
ATACTCTTACTTTAATGGCATTTTTTA
Found at i:411014 original size:92 final size:91
Alignment explanation
Indices: 410816--411014 Score: 238
Period size: 92 Copynumber: 2.2 Consensus size: 91
410806 GTTTTGTTCG
* * *
410816 ACAAACGCCATAATAGATATGTATAACATCATTTTTAGCGGCGTTTTTGATCAAACACCATAAAA
1 ACAAACGCCATAATAGAGATGTATAACATCATTTTTAGCAGCGTTTTTGATCAAACACCACAAAA
* *
410881 TACTCTTACTTTAGTGGCATTTTTTA
66 TACTCTTACTTTAATGGCATTTTATA
* * * * * **
410907 ACAAACGCCGTAATAGAGATGTATATCGTTATTTTTAGCAGCGTTTTTTTATCAAACGTCACAAA
1 ACAAACGCCATAATAGAGATGTATAACATCATTTTTAGCAGCG-TTTTTGATCAAACACCACAAA
*
410972 ATACTCTTACTTTAATGGCGTTTGTAT-
65 ATACTCTTACTTTAATGGCATTT-TATA
* *
410999 ACAAACACCACAATAG
1 ACAAACGCCATAATAG
411015 TCATGTACTT
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
91 37 0.41
92 51 0.57
93 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (91 bp):
ACAAACGCCATAATAGAGATGTATAACATCATTTTTAGCAGCGTTTTTGATCAAACACCACAAAA
TACTCTTACTTTAATGGCATTTTATA
Found at i:414347 original size:19 final size:19
Alignment explanation
Indices: 414323--414366 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
414313 AGAAGTAGAG
*
414323 AGAGAAAAAGAGATAAGCA
1 AGAGAAAAAGAGAGAAGCA
** *
414342 AGAGAATTAGAGAGCAGCA
1 AGAGAAAAAGAGAGAAGCA
414361 AGAGAA
1 AGAGAA
414367 GCGGAGAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.07, G:0.30, T:0.07
Consensus pattern (19 bp):
AGAGAAAAAGAGAGAAGCA
Found at i:414809 original size:42 final size:42
Alignment explanation
Indices: 414763--414884 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
414753 AAAAACGTCA
*
414763 CTAAATGACCTACCTATTACGGTGTTTGTGCACGAAACGCCG
1 CTAAATGACCTACCTATTACGGCGTTTGTGCACGAAACGCCG
** * * * *
414805 CTAAAT-ATCAAATCTGTTACGGCGTTTGTG-ACTAAAAATGCCG
1 CTAAATGA-CCTACCTATTACGGCGTTTGTGCAC--GAAACGCCG
*
414848 CTAAATGACCTACCTATTGCGGCGTTTGTGCACGAAA
1 CTAAATGACCTACCTATTACGGCGTTTGTGCACGAAA
414885 TGTCACTAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
41 3 0.05
42 26 0.42
43 30 0.48
44 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (42 bp):
CTAAATGACCTACCTATTACGGCGTTTGTGCACGAAACGCCG
Found at i:414953 original size:85 final size:85
Alignment explanation
Indices: 414752--414938 Score: 275
Period size: 85 Copynumber: 2.2 Consensus size: 85
414742 CGTTTTTAGG
* * * * *
414752 TAAAAACGTCACTAAATGACCTACCTATTACGGTGTTTGTGCACGAAACGCCGCTAAATATCAAA
1 TAAAAACGCCGCTAAATGACCTACCTATTGCGGCGTTTGTGCACGAAACGCCACTAAATATCAAA
*
414817 TCTGTTACGGCGTTTGTGAC
66 TATGTTACGGCGTTTGTGAC
* * *
414837 TAAAAATGCCGCTAAATGACCTACCTATTGCGGCGTTTGTGCACGAAATGTCACTAAATATCAAA
1 TAAAAACGCCGCTAAATGACCTACCTATTGCGGCGTTTGTGCACGAAACGCCACTAAATATCAAA
**
414902 TATGTTGTGGCGTTTGTGAC
66 TATGTTACGGCGTTTGTGAC
414922 TAAAAACGCCGCTAAAT
1 TAAAAACGCCGCTAAAT
414939 AGTGAACCTC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (85 bp):
TAAAAACGCCGCTAAATGACCTACCTATTGCGGCGTTTGTGCACGAAACGCCACTAAATATCAAA
TATGTTACGGCGTTTGTGAC
Found at i:418596 original size:29 final size:30
Alignment explanation
Indices: 418541--418606 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
418531 ACTTTAGTCC
*
418541 CTTAACTTTTCTAAAATTTCTACTTTGGCCA
1 CTTAAC-TTTCTAAAATTTATACTTTGGCCA
* *
418572 CTTAACTTTC-AAAATTTATATTTTGGTCA
1 CTTAACTTTCTAAAATTTATACTTTGGCCA
418601 C-TAACT
1 CTTAACT
418607 AAAATTTGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 5 0.16
29 17 0.53
30 4 0.12
31 6 0.19
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (30 bp):
CTTAACTTTCTAAAATTTATACTTTGGCCA
Found at i:427493 original size:35 final size:34
Alignment explanation
Indices: 427451--427519 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
427441 ACCTAAAGCC
* *
427451 AATAAGGTACCTAGAGAAATGGAAATGAAAGCCAA
1 AATAAGGTACCCACAGAAATGGAAA-GAAAGCCAA
* *
427486 AATAAGGTGCCCACAGAAATGGAAAGGAAGCCAA
1 AATAAGGTACCCACAGAAATGGAAAGAAAGCCAA
427520 TGAGCAGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 8 0.27
35 22 0.73
ACGTcount: A:0.49, C:0.14, G:0.25, T:0.12
Consensus pattern (34 bp):
AATAAGGTACCCACAGAAATGGAAAGAAAGCCAA
Found at i:434894 original size:27 final size:26
Alignment explanation
Indices: 434861--434916 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
434851 AGTTTTATAA
434861 AAGTTTTCTC-TTTTAT-TTTTACTTTTC
1 AAGTTTT-TCATTTT-TCTTTTA-TTTTC
434888 AAGTTTTTCATTTTTCTTTTATTTTC
1 AAGTTTTTCATTTTTCTTTTATTTTC
434914 AAG
1 AAG
434917 CTTTGTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.18, C:0.12, G:0.05, T:0.64
Consensus pattern (26 bp):
AAGTTTTTCATTTTTCTTTTATTTTC
Found at i:435312 original size:20 final size:20
Alignment explanation
Indices: 435284--435328 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
435274 AAACGGTAAA
*
435284 TGATCTACGACAATTGATGT
1 TGATTTACGACAATTGATGT
*
435304 TGATTTACGATAATTGATGT
1 TGATTTACGACAATTGATGT
435324 TGATT
1 TGATT
435329 AGATCAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (20 bp):
TGATTTACGACAATTGATGT
Found at i:444711 original size:30 final size:30
Alignment explanation
Indices: 444677--444751 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
444667 AAATGGATTT
** * *
444677 AGTTTAGTGATTAAATTATAAGATTTTG-AA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAAA
*
444707 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
*
444737 AGTTTAGCGACCAAA
1 AGTTTAGTGACCAAA
444752 ATGTAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:445560 original size:30 final size:31
Alignment explanation
Indices: 445524--445588 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
445514 TAGGCCTTAT
* * *
445524 AAAAATTTGAGGA-TCATTTTATAATTTTTG
1 AAAAATTGGAGGACTAATTTTATAATTTTGG
* *
445554 AAAAATTGGGGGACTAATTTTGTAATTTTGG
1 AAAAATTGGAGGACTAATTTTATAATTTTGG
445585 AAAA
1 AAAA
445589 GTTATTAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.40
Consensus pattern (31 bp):
AAAAATTGGAGGACTAATTTTATAATTTTGG
Found at i:447123 original size:31 final size:31
Alignment explanation
Indices: 446879--447129 Score: 358
Period size: 31 Copynumber: 8.1 Consensus size: 31
446869 GAGTCGAGGG
* * * *
446879 TTACCTATGTTCTTCGAGACATGTGGATAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* * *
446910 TTACCTATGTTCTTTGGGACATATGGATAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
446941 TTACCTATGTTCTTTGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
446972 TTACTTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
447003 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
447034 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
447065 TTACCTATGTTCTTCGAGACATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
447096 TTACTTATGTTCTTCGGGACATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
447127 TTA
1 TTA
447130 TTATACGAGC
Statistics
Matches: 206, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 206 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:448909 original size:19 final size:20
Alignment explanation
Indices: 448882--448921 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
448872 TCACAATCTT
448882 AATTCGCTTATT-TTTATTTA
1 AATTCGCTT-TTATTTATTTA
448902 AATT-GCTTTTATTTATTTA
1 AATTCGCTTTTATTTATTTA
448921 A
1 A
448922 TCATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
AATTCGCTTTTATTTATTTA
Found at i:448947 original size:18 final size:19
Alignment explanation
Indices: 448894--448948 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
448884 TTCGCTTATT
448894 TTTATTTAAAT-TGCTTTTA
1 TTTATTTAAATAT-CTTTTA
448913 TTTATTT-AATCAT-TTTTA
1 TTTATTTAAAT-ATCTTTTA
448931 -TTATTTAAATATCTTTTA
1 TTTATTTAAATATCTTTTA
448949 CCAAACCCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 8 0.25
18 16 0.50
19 7 0.22
20 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTATTTAAATATCTTTTA
Found at i:458014 original size:15 final size:15
Alignment explanation
Indices: 457991--458030 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
457981 GAGGGGGAAT
457991 AGAAGAAGAAGAAAA
1 AGAAGAAGAAGAAAA
*
458006 AGAATAAGAAGAAAA
1 AGAAGAAGAAGAAAA
*
458021 AAAAGAAGAA
1 AGAAGAAGAA
458031 TGAAGTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AGAAGAAGAAGAAAA
Found at i:458016 original size:18 final size:18
Alignment explanation
Indices: 457993--458027 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
457983 GGGGGAATAG
*
457993 AAGAAGAAGAAAAAGAAT
1 AAGAAGAAAAAAAAGAAT
458011 AAGAAGAAAAAAAAGAA
1 AAGAAGAAAAAAAAGAA
458028 GAATGAAGTC
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:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AAGAAGAAAAAAAAGAAT
Found at i:458133 original size:28 final size:28
Alignment explanation
Indices: 458102--458186 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 28
458092 TAAATGAATT
*
458102 TATGAATTTGGGTTTAGTTAAATATATG
1 TATGAATTTGAGTTTAGTTAAATATATG
458130 TATGAATTTGAGTTTAGTTAAATATATG
1 TATGAATTTGAGTTTAGTTAAATATATG
* * *
458158 TATGAATTTGAGCTTATTTATATATATG
1 TATGAATTTGAGTTTAGTTAAATATATG
458186 T
1 T
458187 TTATTGATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (28 bp):
TATGAATTTGAGTTTAGTTAAATATATG
Found at i:460282 original size:23 final size:23
Alignment explanation
Indices: 460255--460298 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
460245 ACGAAAAATG
460255 TCAAAAAGA-ACCATTAATAATCT
1 TCAAAAA-ATACCATTAATAATCT
*
460278 TCAAAAAATGCCATTAATAAT
1 TCAAAAAATACCATTAATAAT
460299 GTACCATGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (23 bp):
TCAAAAAATACCATTAATAATCT
Found at i:462232 original size:12 final size:14
Alignment explanation
Indices: 462207--462282 Score: 53
Period size: 12 Copynumber: 6.1 Consensus size: 14
462197 TAGATATAGA
462207 TTATTCTATATTAT
1 TTATTCTATATTAT
462221 TTATT-TAT-TTAT
1 TTATTCTATATTAT
*
462233 TTATTAT-TATTA-
1 TTATTCTATATTAT
*
462245 TTATTAT-TATTA-
1 TTATTCTATATTAT
*
462257 TTATTAT-TATTA-
1 TTATTCTATATTAT
*
462269 TTATTAT-TATTAT
1 TTATTCTATATTAT
462282 T
1 T
462283 ATATATATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
12 46 0.78
13 8 0.14
14 5 0.08
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTCTATATTAT
Found at i:462239 original size:3 final size:3
Alignment explanation
Indices: 462233--462284 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
462223 ATTTATTTAT
462233 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
462281 TTA T
1 TTA T
462285 ATATATAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:462792 original size:13 final size:13
Alignment explanation
Indices: 462774--462808 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
462764 TCATTAACTA
462774 TTGACTTTTATCG
1 TTGACTTTTATCG
*
462787 TTGACTTTGATCG
1 TTGACTTTTATCG
462800 TTGACTTTT
1 TTGACTTTT
462809 TTAAAAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.54
Consensus pattern (13 bp):
TTGACTTTTATCG
Found at i:463429 original size:29 final size:29
Alignment explanation
Indices: 463409--463550 Score: 196
Period size: 29 Copynumber: 4.9 Consensus size: 29
463399 TTATATTCAC
* * *
463409 GTCTTGATTTTACATGAGATTATGTCCTT
1 GTCTTGATTCTGCATGAGATTATATCCTT
463438 GTCTTGATTCTGCATGAGATTATATCCTT
1 GTCTTGATTCTGCATGAGATTATATCCTT
*
463467 GTCCTGATTCTGCATGAGATTATATCCTT
1 GTCTTGATTCTGCATGAGATTATATCCTT
* * * *
463496 GTCCTGATTCTACATGAGATTATGTCCAT
1 GTCTTGATTCTGCATGAGATTATATCCTT
463525 GT-TCTGATTCTGCATGAGATTATATC
1 GTCT-TGATTCTGCATGAGATTATATC
463551 ATCGTCCTAT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
29 102 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (29 bp):
GTCTTGATTCTGCATGAGATTATATCCTT
Found at i:464843 original size:2 final size:2
Alignment explanation
Indices: 464836--464864 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
464826 ATAAATAAAT
464836 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
464865 TAAATTGTAG
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:475475 original size:15 final size:15
Alignment explanation
Indices: 475448--475605 Score: 98
Period size: 15 Copynumber: 10.3 Consensus size: 15
475438 GCTTGAAGAA
*
475448 AAAAAGAGAAAAAAGG
1 AAAAAG-GAAAAAAAG
*
475464 AAAAA-AAGAAAAAAG
1 AAAAAGGA-AAAAAAG
475479 AAAAAAGG-AAAAAAG
1 -AAAAAGGAAAAAAAG
475494 AAAAAAGG-AAAAAAG
1 -AAAAAGGAAAAAAAG
475509 -AAAAGGAAAAAAGAG
1 AAAAAGGAAAAAA-AG
**
475524 AAAAAATGG-AAAAGTG
1 -AAAAA-GGAAAAAAAG
*
475540 AAAAAGG-GAAAAA-
1 AAAAAGGAAAAAAAG
*
475553 AAAAAGGAAAAAATG
1 AAAAAGGAAAAAAAG
475568 AAAAAGAGAAAAATGAAG
1 AAAAAG-GAAAAA--AAG
*
475586 -AAAAGAAAAAAAATG
1 AAAAAGGAAAAAAA-G
475601 AAAAA
1 AAAAA
475606 ATGGAAGAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
13 13 0.11
14 17 0.15
15 42 0.37
16 26 0.23
17 13 0.11
18 4 0.03
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (15 bp):
AAAAAGGAAAAAAAG
Found at i:475597 original size:8 final size:8
Alignment explanation
Indices: 475443--475597 Score: 97
Period size: 8 Copynumber: 19.2 Consensus size: 8
475433 ATTTTGCTTG
475443 AAGAAAAA
1 AAGAAAAA
475451 AAGAGAAAA
1 AAGA-AAAA
475460 AAGGAAAAA
1 AA-GAAAAA
475469 AAG-AAAA
1 AAGAAAAA
475476 AAG-AAAA
1 AAGAAAAA
*
475483 AAGGAAAA
1 AAGAAAAA
475491 AAG-AAAA
1 AAGAAAAA
*
475498 AAGGAAAA
1 AAGAAAAA
475506 AAG--AAA
1 AAGAAAAA
*
475512 AGGAAAAA
1 AAGAAAAA
475520 AGAGAAAAA
1 A-AGAAAAA
* *
475529 ATGGAAAA
1 AAGAAAAA
**
475537 GTGAAAAA
1 AAGAAAAA
*
475545 GGGAAAAAAAA
1 ---AAGAAAAA
475556 AAGGAAAAA
1 AA-GAAAAA
*
475565 ATGAAAAA
1 AAGAAAAA
*
475573 GAG-AAAA
1 AAGAAAAA
* *
475580 ATGAAGAA
1 AAGAAAAA
475588 AAGAAAAA
1 AAGAAAAA
475596 AA
1 AA
475598 ATGAAAAAAT
Statistics
Matches: 117, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
6 5 0.04
7 26 0.22
8 54 0.46
9 25 0.21
10 2 0.02
11 5 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:475616 original size:18 final size:18
Alignment explanation
Indices: 475560--475606 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
475550 AAAAAAAAGG
475560 AAAAAATG-A-AAAAG-A
1 AAAAAATGAAGAAAAGAA
*
475575 GAAAAATGAAGAAAAGAA
1 AAAAAATGAAGAAAAGAA
475593 AAAAAATGAA-AAAA
1 AAAAAATGAAGAAAA
475607 TGGAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.26
16 1 0.04
17 9 0.33
18 10 0.37
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAATGAAGAAAAGAA
Found at i:475623 original size:7 final size:7
Alignment explanation
Indices: 475448--475596 Score: 113
Period size: 7 Copynumber: 19.9 Consensus size: 7
475438 GCTTGAAGAA
475448 AAAAAGAG
1 AAAAA-AG
475456 AAAAAAGG
1 AAAAAA-G
475464 AAAAAAAG
1 -AAAAAAG
475472 AAAAAAG
1 AAAAAAG
475479 AAAAAAGG
1 AAAAAA-G
475487 AAAAAAG
1 AAAAAAG
475494 AAAAAAGG
1 AAAAAA-G
475502 AAAAAAG
1 AAAAAAG
475509 AAAAGGAA-
1 AAAA--AAG
*
475517 AAAAGAG
1 AAAAAAG
475524 AAAAAATGG
1 AAAAAA--G
**
475533 AAAAGTG
1 AAAAAAG
*
475540 AAAAAGG
1 AAAAAAG
*
475547 GAAAAA-
1 AAAAAAG
*
475553 AAAAAGG
1 AAAAAAG
475560 AAAAAATG
1 AAAAAA-G
475568 AAAAAGAG
1 AAAAA-AG
*
475576 AAAAATG
1 AAAAAAG
475583 AAGAAAAG
1 AA-AAAAG
475591 AAAAAA
1 AAAAAA
475597 AATGAAAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 27
0.74 0.08 0.17
Matches are distributed among these distances:
6 5 0.04
7 53 0.46
8 43 0.37
9 14 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:475628 original size:10 final size:9
Alignment explanation
Indices: 475446--475529 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
475436 TTGCTTGAAG
475446 AAAAAAAGA
1 AAAAAAAGA
* *
475455 GAAAAAAGG
1 AAAAAAAGA
475464 AAAAAAAG-
1 AAAAAAAGA
475472 -AAAAAAG-
1 AAAAAAAGA
475479 -AAAAAAG-
1 AAAAAAAGA
*
475486 GAAAAAAGA
1 AAAAAAAGA
475495 AAAAAGGAA-A
1 AAAAA--AAGA
475505 AAAGAAAAGGA
1 AAA-AAAA-GA
*
475516 AAAAAGAGA
1 AAAAAAAGA
475525 AAAAA
1 AAAAA
475530 TGGAAAAGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
7 14 0.22
8 7 0.11
9 27 0.43
10 7 0.11
11 8 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:476928 original size:37 final size:37
Alignment explanation
Indices: 476868--476976 Score: 148
Period size: 37 Copynumber: 2.9 Consensus size: 37
476858 AAGTCAAGCT
* * * *
476868 TAAGCCTTCACGAAAGAGCAGTGAATCAATTCAATC-A
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATC-ATCTA
*
476905 TAAGCCTTCACGGAATAGTAGTGAAGCAAATCATCTA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCATCTA
476942 TAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCAT
1 TAAGCCTTCACGGAAGAGTAGTGAAGC-AAATCAT
476977 TTTATGAAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 3 0.05
37 54 0.84
38 7 0.11
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (37 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCATCTA
Found at i:477114 original size:106 final size:106
Alignment explanation
Indices: 476981--477553 Score: 635
Period size: 106 Copynumber: 5.4 Consensus size: 106
476971 AATCATTTTA
* * *
476981 TGAAGATCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGATACATTTGTTGAAGATTGTTCAA
1 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTGTTGAAGATTGTTCGA
*
477046 GTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTAT
66 GTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
* * * *
477087 TGAAGATCGAGTCCTATACTCTCTGAAGCAATGGGGAGCAGACATATTTGTTGAAGA----TCGA
1 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTGTTGAAGATTGTTCGA
* **
477148 GTCCTATACTCTTTGAAGGAATATAGAGCAGACACGTTTGT
66 GTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
* *
477189 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTGTTGAAGA----TCGA
1 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTGTTGAAGATTGTTCGA
* * *
477250 GTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTTGT
66 GTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
* * *
477291 TGAAGATTGTTTGAGTCCTATACTCTCTGATGGAATAGGGAGCGAACACGA-TTGTTGAAGATTG
1 TGAAGA----TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-ATTTGTTGAAGATTG
*
477355 TTCGAGTTCTATACTCTCTGAAGGAATAGGGAGC-GTACACGTTTGT
61 TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAG-ACACGTTTGT
* * * *
477401 TGAAGATCGAGTCCTATACTCTTTGAAGGAATAGAGAGCGGACACGTTTGTTCAAGATTGTTCGA
1 TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTGTTGAAGATTGTTCGA
** * * * * * * * * *
477466 GTATTATATTCCCTGAATGAATATGGCGCGGACCCGTATGC
66 GTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
* * * *
477507 TGAAGATTATTCGAGTCTTATACTCCCTGAAGGAATATGGAGTGGAC
1 TGAAG---A-TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
477554 CTGTCATTCG
Statistics
Matches: 399, Mismatches: 52, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
102 138 0.35
106 181 0.45
107 1 0.00
109 2 0.01
110 77 0.19
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (106 bp):
TGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTGTTGAAGATTGTTCGA
GTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
Found at i:477554 original size:55 final size:55
Alignment explanation
Indices: 476987--477553 Score: 607
Period size: 51 Copynumber: 10.7 Consensus size: 55
476977 TTTATGAAGA
* * *
476987 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGATACATTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * *
477042 TCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGA----
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * **
477093 TCGAGTCCTATACTCTCTGAAGCAATGGGGAGCAGACATATTTGTTGAAGA----
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* ** *
477144 TCGAGTCCTATACTCTTTGAAGGAATATAGAGCAGACACGTTTGTTGAAGA----
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* *
477195 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTGTTGAAGA----
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* *
477246 TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
477301 TTGAGTCCTATACTCTCTGATGGAATAGGGAGCGAACACGATTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* *
477356 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGTACACGTTTGTTGAAGA----
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * *
477407 TCGAGTCCTATACTCTTTGAAGGAATAGAGAGCGGACACGTTTGTTCAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
** * * * * * * * * *
477462 TCGAGTATTATATTCCCTGAATGAATATGGCGCGGACCCGTATGCTGAAGATTAT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
477517 TCGAGTCTTATACTCCCTGAAGGAATATGGAGTGGAC
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
477554 CTGTCATTCG
Statistics
Matches: 443, Mismatches: 61, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
51 230 0.52
55 213 0.48
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
Found at i:477579 original size:55 final size:55
Alignment explanation
Indices: 477144--477554 Score: 213
Period size: 55 Copynumber: 7.7 Consensus size: 55
477134 TTGTTGAAGA
* ** * * * * *
477144 TCGAGTCCTATACTCTTTGAAGGAATATAGAGCAGACACGTTTGTTGAAG---A-
1 TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACCCGTATGCTGAAGATTAT
* * * * * * * *
477195 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTGTTGAAG---A-
1 TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACCCGTATGCTGAAGATTAT
* * * * * * * * *
477246 TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACATTTGTTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACCCGTATGCTGAAGATTAT
* * * * * * * * *
477301 TTGAGTCCTATACTCTCTGATGGAATAGGGAGCGAACACG-ATTGTTGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACCCGTA-TGCTGAAGATTAT
* * * * * *
477356 TCGAGT-TCTATACTCTCTGAAGGAATAGGGAGCGTACACGTTTGTTGAAG---A-
1 TCGAGTCT-TATACTCCCTGAAGGAATATGGAGCGGACCCGTATGCTGAAGATTAT
* ** * * * * *
477407 TCGAGTCCTATACTCTTTGAAGGAATA-GAGAGCGGACACGTTTGTTCAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATATG-GAGCGGACCCGTATGCTGAAGATTAT
* * * *
477462 TCGAGTATTATATTCCCTGAATGAATATGGCGCGGACCCGTATGCTGAAGATTAT
1 TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACCCGTATGCTGAAGATTAT
*
477517 TCGAGTCTTATACTCCCTGAAGGAATATGGAGTGGACC
1 TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACC
477555 TGTCATTCGA
Statistics
Matches: 304, Mismatches: 42, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
50 1 0.00
51 137 0.45
55 165 0.54
56 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
TCGAGTCTTATACTCCCTGAAGGAATATGGAGCGGACCCGTATGCTGAAGATTAT
Found at i:478099 original size:16 final size:16
Alignment explanation
Indices: 478078--478110 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
478068 CAGAAACGAA
478078 AAAGAACTAGAGAGAT
1 AAAGAACTAGAGAGAT
478094 AAAGAACTAGAGAGAT
1 AAAGAACTAGAGAGAT
478110 A
1 A
478111 TCTGTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAGAACTAGAGAGAT
Found at i:480215 original size:2 final size:2
Alignment explanation
Indices: 480208--480236 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
480198 GCCTAAAATA
480208 AT 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 AT A
480237 ATTATTAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:486655 original size:21 final size:22
Alignment explanation
Indices: 486610--486670 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
486600 ATTGCTCAGA
486610 GGGAACCGATTCCCCCCTAAGG
1 GGGAACCGATTCCCCCCTAAGG
486632 GGGAACCGATTCCCCCCTAAGG
1 GGGAACCGATTCCCCCCTAAGG
* *
486654 GGGTACCGATCCCCCCC
1 GGGAACCGATTCCCCCC
486671 CCTAAATGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.20, C:0.41, G:0.26, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTAAGG
Found at i:492515 original size:20 final size:19
Alignment explanation
Indices: 492490--492549 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 19
492480 TTTTGGCGCA
*
492490 GAGGGAATCGATCTCCCCTT
1 GAGGGAACCGAT-TCCCCTT
492510 GAGGGAACCGATTCCCCTTTT
1 GAGGGAACCGATTCCCC--TT
492531 GAAGGGGAACCGATTCCCC
1 G-A-GGGAACCGATTCCCC
492550 CCACAGGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 3 0.09
22 1 0.03
23 15 0.43
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCTT
Found at i:499692 original size:2 final size:2
Alignment explanation
Indices: 499685--499730 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
499675 ATATTTAAAA
499685 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
499727 AT AT
1 AT AT
499731 GATTATAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:508290 original size:19 final size:21
Alignment explanation
Indices: 508266--508305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
508256 TAGGCATTTT
508266 TACATGCA-TTA-ATCATGGA
1 TACATGCATTTATATCATGGA
*
508285 TACATGGATTTATATCATGGA
1 TACATGCATTTATATCATGGA
508306 GGACTATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
TACATGCATTTATATCATGGA
Found at i:509346 original size:43 final size:47
Alignment explanation
Indices: 509298--509404 Score: 125
Period size: 50 Copynumber: 2.3 Consensus size: 47
509288 ATAACCAATG
509298 AATAAAATAATAACAAACT-AAA-T-ATGTCTTAACT-C-TAATTCCT
1 AATAAAATAATAA-AAACTAAAATTAATGTCTTAACTACTTAATTCCT
* *
509341 AATAAAATAATAATAACTAAAATTAATGTTTTAACTCAACCTTAATTCCT
1 AATAAAATAATAAAAACTAAAATTAATGTCTTAACT--A-CTTAATTCCT
509391 AATAAAATAATAAA
1 AATAAAATAATAAA
509405 TCTAATCCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
42 4 0.08
43 16 0.30
44 1 0.02
45 10 0.19
49 1 0.02
50 21 0.40
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (47 bp):
AATAAAATAATAAAAACTAAAATTAATGTCTTAACTACTTAATTCCT
Found at i:513056 original size:66 final size:65
Alignment explanation
Indices: 512818--513056 Score: 245
Period size: 66 Copynumber: 3.6 Consensus size: 65
512808 TTCTATTAAA
* * *
512818 AAACAAATTTTGTCTCACTTGAGACAGACTTC-CTT-AAGACAT-ATCTTTGAGATTGTTTCTCT
1 AAACAAATTTTGTCTCTCTTGAGAAAG-TTTCTCTTGAA-ACATAATCTTTGAGATTGTTTCTCT
512880 TG
64 TG
* * *
512882 AAACAAATTTTGTCTCTCTTGAGACAA-TTTATCTTGAAACATAAAACTTTGAGATTGTTTCTAT
1 AAACAAATTTTGTCTCTCTTGAGA-AAGTTTCTCTTGAAACAT-AATCTTTGAGATTGTTTCTCT
512946 TG
64 TG
***** * **
512948 AATTTTTTTTTTTGTCTATCTTGAGTCAGTTTCTCTTGAAACATACATCTTTGAGATTGTTTAC-
1 AA--ACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACATA-ATCTTTGAGATTGTTT-CT
513012 CTTG
62 CTTG
513016 AAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACA
1 AAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACA
513057 AAATATTCCC
Statistics
Matches: 140, Mismatches: 25, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
63 2 0.01
64 30 0.21
65 3 0.02
66 53 0.38
67 2 0.01
68 49 0.35
69 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (65 bp):
AAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACATAATCTTTGAGATTGTTTCTCTTG
Found at i:513311 original size:138 final size:137
Alignment explanation
Indices: 513063--513603 Score: 704
Period size: 138 Copynumber: 3.9 Consensus size: 137
513053 AACAAAATAT
* ** * *
513063 TCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCACATACCATATCACTTC
1 TCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATC-TTTC
* * * *
513128 ATCACGTAGGAGCAGCCTCATCCTTAGATAGCCAGACTTCCTCATCACGTAGGAACTGTGTTATA
65 ATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACTGTGTTATC
*
513193 TCTATTTA
130 TCCATTTA
*
513201 TCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACCAGATCTTGTC
1 TCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTT-TC
* * * * * **
513266 ATCACATAGGAGCAACATCATTCTTAGATAGCCAAACTTCCTCATCACGTAGGAACCATGTTATC
65 ATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACTGTGTTATC
513331 TCCATTTA
130 TCCATTTA
* ** *
513339 TTCCTAAAGATGGCTAGATATCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTCCTC
1 TCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCT-TTC
* ** * *
513404 ATCGCGTAGGAGCAGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAAGAACTGAGTTATC
65 ATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACTGTGTTATC
513469 TCCATTTA
130 TCCATTTA
* * * *
513477 TCCTTAAAGATGGCTAGACTTCCTCATCACGTAAGAACAATGTCATCCACCAACCAGATCTCTTC
1 TCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCT-TTC
* * * * * * *
513542 TTAACGTAGAATCAATGTCATCCTTAGATAACCGGACTTCCTCATCATGTAGGAACTGTGTT
65 ATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACTGTGTT
513604 GTCTTCAAAT
Statistics
Matches: 352, Mismatches: 49, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
137 1 0.00
138 351 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (137 bp):
TCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTTTCA
TCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACTGTGTTATCT
CCATTTA
Found at i:513940 original size:3 final size:3
Alignment explanation
Indices: 513932--513972 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
513922 ATTTATTAAT
* * *
513932 TTA TTA TTA TTA TTA TCA CTA TTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
513973 TATAATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:527328 original size:35 final size:35
Alignment explanation
Indices: 527279--527346 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
527269 AAGTCTCTGC
527279 AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
1 AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
*
527314 AGGTTCAGAC-CGATCGAACTGGTAATTCCTTAT
1 AGGTTCAG-CTCGATCAAACTGGTAATTCCTTAT
527347 GGACCTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (35 bp):
AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
Found at i:530745 original size:13 final size:13
Alignment explanation
Indices: 530727--530751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530717 ACCAGTGTTA
530727 ACCGTTAACTTTG
1 ACCGTTAACTTTG
530740 ACCGTTAACTTT
1 ACCGTTAACTTT
530752 TACTTTGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
ACCGTTAACTTTG
Found at i:532075 original size:28 final size:28
Alignment explanation
Indices: 532044--532104 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
532034 TGATTCCATA
**
532044 TGATTTATCTGATTTAAAGTCTGATT-TC
1 TGATTTATAAGATTT-AAGTCTGATTGTC
*
532072 TGATTTATAAGGTTTAAGTCTGATTGTC
1 TGATTTATAAGATTTAAGTCTGATTGTC
532100 TGATT
1 TGATT
532105 CCTGTTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (28 bp):
TGATTTATAAGATTTAAGTCTGATTGTC
Found at i:538043 original size:18 final size:18
Alignment explanation
Indices: 538020--538057 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
538010 AAACACATAC
*
538020 CTTTTCTAGAGTTTTCCT
1 CTTTTCCAGAGTTTTCCT
538038 CTTTTCCAGAGTTTTCCT
1 CTTTTCCAGAGTTTTCCT
538056 CT
1 CT
538058 GGTCCGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.53
Consensus pattern (18 bp):
CTTTTCCAGAGTTTTCCT
Found at i:543689 original size:8 final size:8
Alignment explanation
Indices: 543676--543702 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
543666 ACCAATTAAT
543676 AAGAATGA
1 AAGAATGA
543684 AAGAATGA
1 AAGAATGA
543692 AAGAATGA
1 AAGAATGA
543700 AAG
1 AAG
543703 GGCATTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (8 bp):
AAGAATGA
Found at i:544819 original size:21 final size:20
Alignment explanation
Indices: 544776--544821 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
544766 ATGTTTGGCA
* **
544776 AAACTCACTTTCCTTGTTTT
1 AAACTCACTTTCCCTCATTT
544796 AAACTCACTTTCCCCTCATTT
1 AAACTCACTTT-CCCTCATTT
544817 AAACT
1 AAACT
544822 AGTTGCCACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.41
Consensus pattern (20 bp):
AAACTCACTTTCCCTCATTT
Found at i:549586 original size:19 final size:17
Alignment explanation
Indices: 549559--549610 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 17
549549 CGAACCGACT
*
549559 CGTTAACTTTGACCCAA
1 CGTTGACTTTGACCCAA
549576 CCCGTTGACTTTGA-CCAGA
1 --CGTTGACTTTGACCCA-A
549595 -GTTGACTTTGACCCAA
1 CGTTGACTTTGACCCAA
549611 AAAGTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 12 0.40
17 3 0.10
18 3 0.10
19 12 0.40
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (17 bp):
CGTTGACTTTGACCCAA
Found at i:551539 original size:60 final size:60
Alignment explanation
Indices: 551446--551853 Score: 483
Period size: 60 Copynumber: 6.8 Consensus size: 60
551436 AATTGCTCTA
*
551446 AGATGAAAAGTTAAATGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* ** * * * *
551506 AGATGAAAAGTTAAATGCCTAACGAAGCATTTTGGCAGAAATCTACAATTATTGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * * * *
551566 AGATGAAAAGTTAATTGCCTAACGATGCATTATGGGATAAAGGTTCCATTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * * *
551626 AGATGAAAGGTTAAATGCCTAATGGTGCATTTTGCCAGAAAGGTGCCACTATTGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * *
551686 AGATGAAAAGTTAATTGCCTAACGATGCATTTTGGCTGAAAGGTGCCACTATTGTAAGTT
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * * * * * * * *
551746 AGATGAGAATTTAATTGCTTAACAATGCATTTTGACATAAAAGTGACACTAATGTAAGTT
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * *
551806 AGATGAAAGGTTAAATGTCTAATGGTGCATTTTGGCAGAAAGGTGCCA
1 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCA
551854 AAAGGTGCCA
Statistics
Matches: 289, Mismatches: 59, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 289 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (60 bp):
AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
Found at i:551748 original size:180 final size:180
Alignment explanation
Indices: 551446--551853 Score: 566
Period size: 180 Copynumber: 2.3 Consensus size: 180
551436 AATTGCTCTA
* *
551446 AGATGAAAAGTTAAATGCCTAACT-ATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGAT
1 AGATGAAAGGTTAAATGCCTAA-TGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGAT
* *
551510 GAAAAGTTAAATGCCTAACGAAGCATTTTGGCAGAAATCTACAATTATTGCAAGTTAGATGAAAA
65 GAAAAGTTAAATGCCTAACGAAGCATTTTGGCAGAAAGCTACAACTATTGCAAGTTAGATGAAAA
* ** * ** *
551575 GTTAATTGCCTAACGATGCATTATGGGATAAAGGTTCCATTAATGCAAGTT
130 GTTAATTGCCTAACAATGCATTATGACATAAAAGTGACACTAATGCAAGTT
* *
551626 AGATGAAAGGTTAAATGCCTAATGGTGCATTTTGCCAGAAAGGTGCCACTATTGCAAGTTAGATG
1 AGATGAAAGGTTAAATGCCTAATGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG
* * * * * * * * *
551691 AAAAGTTAATTGCCTAACGATGCATTTTGGCTGAAAGGTGCCACTATTGTAAGTTAGATGAGAAT
66 AAAAGTTAAATGCCTAACGAAGCATTTTGGCAGAAAGCTACAACTATTGCAAGTTAGATGAAAAG
* * *
551756 TTAATTGCTTAACAATGCATTTTGACATAAAAGTGACACTAATGTAAGTT
131 TTAATTGCCTAACAATGCATTATGACATAAAAGTGACACTAATGCAAGTT
*
551806 AGATGAAAGGTTAAATGTCTAATGGTGCATTTTGGCAGAAAGGTGCCA
1 AGATGAAAGGTTAAATGCCTAATGGTGCATTTTGGCAGAAAGGTGCCA
551854 AAAGGTGCCA
Statistics
Matches: 200, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
179 1 0.00
180 199 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (180 bp):
AGATGAAAGGTTAAATGCCTAATGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATG
AAAAGTTAAATGCCTAACGAAGCATTTTGGCAGAAAGCTACAACTATTGCAAGTTAGATGAAAAG
TTAATTGCCTAACAATGCATTATGACATAAAAGTGACACTAATGCAAGTT
Found at i:564452 original size:26 final size:27
Alignment explanation
Indices: 564422--564474 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
564412 GTCTGAGGTG
*
564422 GCAG-TTTCTAAAAGGTCCAGTCAGCA
1 GCAGTTTTCTAAAAGATCCAGTCAGCA
* *
564448 GCAGTTTTCTAGAAGATCTAGTCAGCA
1 GCAGTTTTCTAAAAGATCCAGTCAGCA
564475 CCTTTTGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (27 bp):
GCAGTTTTCTAAAAGATCCAGTCAGCA
Found at i:568867 original size:3 final size:3
Alignment explanation
Indices: 568861--568919 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
568851 TTTACCCATT
* *
568861 TTA TTA TTA TTA TAA TTA TTA TATA TTA TTA TTA TAA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA
568908 TTA TTA TTA TTA
1 TTA TTA TTA TTA
568920 AAATAATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:568890 original size:22 final size:22
Alignment explanation
Indices: 568862--568917 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
568852 TTACCCATTT
568862 TATTATTATTATAATTATTATA
1 TATTATTATTATAATTATTATA
568884 TATTATTATTATAATTATTATA
1 TATTATTATTATAATTATTATA
568906 TATTATTATTAT
1 TATTATTATTAT
568918 TAAAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTATAATTATTATA
Found at i:574387 original size:15 final size:15
Alignment explanation
Indices: 574369--574400 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
574359 GATCAATACC
574369 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
574384 TTTTGCATACATTCA
1 TTTTGCATACATGCA
574399 TT
1 TT
574401 ATTCAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:581739 original size:1 final size:1
Alignment explanation
Indices: 581733--581783 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
581723 GCTTGAAGAG
* * * * *
581733 AAAAAAAAGAAAAAAAAAAAAAAAAGAGAAAAGAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
581784 GGGGTTCAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:581759 original size:28 final size:27
Alignment explanation
Indices: 581728--581783 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
581718 ATTATGCTTG
581728 AAGAGAAAAAAAAGAAAAAAAAAAAAAA
1 AAGAGAAAAAAAA-AAAAAAAAAAAAAA
* *
581756 AAGAGAAAAGAAAAAAAAAAAAAGAAA
1 AAGAGAAAAAAAAAAAAAAAAAAAAAA
581783 A
1 A
581784 GGGGTTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (27 bp):
AAGAGAAAAAAAAAAAAAAAAAAAAAA
Found at i:581784 original size:19 final size:19
Alignment explanation
Indices: 581733--581784 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
581723 GCTTGAAGAG
581733 AAAAAAAAGAAAA-AAAAA
1 AAAAAAAAGAAAAGAAAAA
581751 AAAAAAAGAGAAAAGAAAAA
1 AAAAAAA-AGAAAAGAAAAA
581771 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
581785 GGGTTCAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.22
19 13 0.41
20 12 0.38
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAGAAAAA
Found at i:582995 original size:94 final size:94
Alignment explanation
Indices: 582787--583163 Score: 661
Period size: 94 Copynumber: 4.0 Consensus size: 94
582777 CGTAGACCCA
* *
582787 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAA-CCCTAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAAACCA
582851 ATCATTGAATTTGGAAGATGAATGTGCTC
66 ATCATTGAATTTGGAAGATGAATGTGCTC
582880 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAAACCA
582945 ATCATTGAATTTGGAAGATGAATGTGCTC
66 ATCATTGAATTTGGAAGATGAATGTGCTC
* *
582974 ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTAATCTGGTTTGGTATGAACCCCAAAAAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAAACCA
*
583039 ATCATTGAATTTGGAAGATGAATATGCTC
66 ATCATTGAATTTGGAAGATGAATGTGCTC
*
583068 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCTC-AAAAA-CA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAAACCA
* *
583131 ATCATTGGATTTGAAAGATGAATGTGCTC
66 ATCATTGAATTTGGAAGATGAATGTGCTC
583160 ATAG
1 ATAG
583164 TAGAAATAAG
Statistics
Matches: 272, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 32 0.12
93 56 0.21
94 184 0.68
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (94 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAAACCA
ATCATTGAATTTGGAAGATGAATGTGCTC
Found at i:583406 original size:115 final size:113
Alignment explanation
Indices: 583065--583344 Score: 508
Period size: 115 Copynumber: 2.4 Consensus size: 113
583055 GATGAATATG
583065 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCTCAAAAAC
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTATGAACCTCAAAAAC
583130 AATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGAC
65 AATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGAC
583179 C-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCTCAAAAA
1 CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTTGGTATGAACCTCAAAAA
583243 TCAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGAC
64 -CAATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGAC
583294 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTA
583345 GAAACCACAG
Statistics
Matches: 161, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
113 2 0.01
114 60 0.37
115 97 0.60
116 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (113 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTATGAACCTCAAAAACA
ATCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAAATAAGAAGAC
Found at i:584306 original size:116 final size:116
Alignment explanation
Indices: 584098--585404 Score: 1950
Period size: 116 Copynumber: 11.3 Consensus size: 116
584088 CAACTTTTCC
* * * * *
584098 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* * * *
584163 ACATTGCCAGGTAGAGTTCATAGTGAGAAGAACTCATCATATGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
584214 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* *
584279 ACATTTCCAATTGGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
* *
584330 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATTACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* *
584395 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
584446 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
*
584511 ACATTTCCAATT-GAAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
*
584562 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* *
584627 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
584678 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* *
584743 ACATTTCCAATTTGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
*
584794 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* *
584859 ACATTTCCAATTTGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
584910 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* *
584975 ACATTTCCAGTTCGAGTTCATATTGAGAAGAA--C-TCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
** * * * **
585023 AGAAGAAGTTCATAATGAGAAGAACTTACTCAACTTTTTGCTTGAATTCATGATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* * * *
585088 GCGTTACCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
* * * * * * * *
585136 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCAACATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
* * *
585201 ACATTGCCAGGTAGAGTTCATAATAAGAAGAACTCATCATCTGAAGAAGGA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
* * * * * *
585252 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
*** ** * * *
585317 GTTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGGAGAA
66 ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
* * *
585365 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACATTTTG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
585405 AATGACTCTA
Statistics
Matches: 1099, Mismatches: 87, Indels: 13
0.92 0.07 0.01
Matches are distributed among these distances:
113 245 0.22
114 2 0.00
115 2 0.00
116 849 0.77
117 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (116 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCA
ACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGA
Found at i:585634 original size:3 final size:3
Alignment explanation
Indices: 585628--585675 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
585618 TTTACCCATT
* *
585628 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
585674 TT
1 TT
585676 TAAAAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:585645 original size:12 final size:12
Alignment explanation
Indices: 585630--585674 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
585620 TACCCATTTT
585630 ATTATTATTATA
1 ATTATTATTATA
585642 ATTATTATTATA
1 ATTATTATTATA
585654 ATTATTA-TAT-
1 ATTATTATTATA
585664 ATTATTATTAT
1 ATTATTATTAT
585675 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.22
11 6 0.19
12 19 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:589516 original size:13 final size:13
Alignment explanation
Indices: 589498--589522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
589488 ATATATATAT
589498 ATTTTAGTAATTC
1 ATTTTAGTAATTC
589511 ATTTTAGTAATT
1 ATTTTAGTAATT
589523 AAAAAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTTAGTAATTC
Found at i:590987 original size:3 final size:3
Alignment explanation
Indices: 590979--591009 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
590969 AAAGTAAAAG
590979 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
591010 CGTATAATGA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:599888 original size:19 final size:20
Alignment explanation
Indices: 599845--599889 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
599835 AGATTTATTA
599845 ATTTAATTTCATATTTCTTT
1 ATTTAATTTCATATTTCTTT
*
599865 ATTTAA-TTCTTATTT-TTT
1 ATTTAATTTCATATTTCTTT
599883 AGTTTAA
1 A-TTTAA
599890 AAACAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTAATTTCATATTTCTTT
Found at i:605489 original size:11 final size:11
Alignment explanation
Indices: 605473--605497 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
605463 AGGCAACCCA
605473 TTTCATTTTAT
1 TTTCATTTTAT
605484 TTTCATTTTAT
1 TTTCATTTTAT
605495 TTT
1 TTT
605498 TTTAGAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:612888 original size:180 final size:181
Alignment explanation
Indices: 612629--612989 Score: 715
Period size: 180 Copynumber: 2.0 Consensus size: 181
612619 TAATTTCTAA
612629 CACAAGCTTCATCAAGCGCATCTTCTTTCTCCACTGATATTCCCTGGCAACCATTCGTTTTGGAC
1 CACAAGCTTCATCAAGCGCATCTTCTTTCTCCACTGATATTCCCTGGCAACCATTCGTTTTGGAC
612694 GTCGTCGTCGGTGCCACATTCTTGGAGAAGTTATAAGATGAGACCAGATCAGTTTCATTTCCGAT
66 GTCGTCGTCGGTGCCACATTCTTGGAGAAGTTATAAGATGAGACCAGATCAGTTTCATTTCCGAT
612759 CTTCCTTCCCCCTTATTCAATTCAAGCCTCGGATCTTTGGGTGTTTTCTTT
131 CTTCCTTCCCCCTTATTCAATTCAAGCCTCGGATCTTTGGGTGTTTTCTTT
612810 CACAAGCTTCATCAAGCGCATCTTCTTTCTCCACTGATA-TCCCTGGCAACCATTCGTTTTGGAC
1 CACAAGCTTCATCAAGCGCATCTTCTTTCTCCACTGATATTCCCTGGCAACCATTCGTTTTGGAC
612874 GTCGTCGTCGGTGCCACATTCTTGGAGAAGTTATAAGATGAGACCAGATCAGTTTCATTTCCGAT
66 GTCGTCGTCGGTGCCACATTCTTGGAGAAGTTATAAGATGAGACCAGATCAGTTTCATTTCCGAT
612939 CTTCCTTCCCCCTTATTCAATTCAAGCCTCGGATCTTTGGGTGTTTTCTTT
131 CTTCCTTCCCCCTTATTCAATTCAAGCCTCGGATCTTTGGGTGTTTTCTTT
612990 TTATCTACAT
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 141 0.78
181 39 0.22
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (181 bp):
CACAAGCTTCATCAAGCGCATCTTCTTTCTCCACTGATATTCCCTGGCAACCATTCGTTTTGGAC
GTCGTCGTCGGTGCCACATTCTTGGAGAAGTTATAAGATGAGACCAGATCAGTTTCATTTCCGAT
CTTCCTTCCCCCTTATTCAATTCAAGCCTCGGATCTTTGGGTGTTTTCTTT
Found at i:614474 original size:26 final size:26
Alignment explanation
Indices: 614438--614487 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
614428 AACTATACCA
*
614438 TATGTTGGTCAATTAATTGTGTTTAG
1 TATGTTGGTCAATTAACTGTGTTTAG
614464 TATGTTGGTCAATTAACTGTGTTT
1 TATGTTGGTCAATTAACTGTGTTT
614488 TCAACATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (26 bp):
TATGTTGGTCAATTAACTGTGTTTAG
Found at i:619197 original size:17 final size:16
Alignment explanation
Indices: 619173--619214 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
619163 GAGAATAATT
619173 AAATAAAATATCA-AA
1 AAATAAAATATCATAA
619188 ATACATAAAAT-TCATAA
1 A-A-ATAAAATATCATAA
619205 AAATAAAATA
1 AAATAAAATA
619215 GGCATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.35
16 5 0.22
17 10 0.43
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAATATCATAA
Found at i:621157 original size:2 final size:2
Alignment explanation
Indices: 621150--621181 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
621140 ATTTTGTTTC
621150 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
621182 ACATTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:621799 original size:54 final size:54
Alignment explanation
Indices: 621717--622032 Score: 479
Period size: 54 Copynumber: 5.9 Consensus size: 54
621707 ACCTAAGCAC
* * *
621717 CGATATGGAAATTCACAAACTCATTATGAATTCCATGGGTTGTACACATAGTGT
1 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
* **
621771 CGATATAGTAATTCACAAACTCATTATGAATTATGTGGGTTGCACACATAGTGT
1 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
*
621825 CGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
1 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
* *
621879 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCAGACATAGTGC
1 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
* * * * *
621933 CGATATGGTAATTCATAAACTCATTATGAATTTCATGAGTTGCACACATAGTGC
1 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
** *
621987 CGATATGGTAATTCACAAACTCATTATGAATTATGTGGGTTACACA
1 CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACA
622033 TATAATGTTG
Statistics
Matches: 238, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 238 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
CGATATGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGT
Found at i:624845 original size:63 final size:63
Alignment explanation
Indices: 624746--624905 Score: 311
Period size: 63 Copynumber: 2.5 Consensus size: 63
624736 CTGTAGATCT
*
624746 TTGATGCAATCCAATAGGGAAGGTCTCAATCTCAATTCTACAATCCATGCACCATCCTTTTCA
1 TTGATGCAATCCAATAGGGAAGGTCTCAATCTCAATTCTACAATCCATGCACAATCCTTTTCA
624809 TTGATGCAATCCAATAGGGAAGGTCTCAATCTCAATTCTACAATCCATGCACAATCCTTTTCA
1 TTGATGCAATCCAATAGGGAAGGTCTCAATCTCAATTCTACAATCCATGCACAATCCTTTTCA
624872 TTGATGCAATCCAATAGGGAAGGTCTCAATCTCA
1 TTGATGCAATCCAATAGGGAAGGTCTCAATCTCA
624906 TTCCATGCAC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 96 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (63 bp):
TTGATGCAATCCAATAGGGAAGGTCTCAATCTCAATTCTACAATCCATGCACAATCCTTTTCA
Found at i:624907 original size:34 final size:34
Alignment explanation
Indices: 624806--624907 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 34
624796 ACCATCCTTT
624806 TCATTGATGCAATCCAATAGGGAAGGTCTCAATC
1 TCATTGATGCAATCCAATAGGGAAGGTCTCAATC
* * * * * *
624840 TCAATT-CTACAATCC-AT--GCACA-ATC-C-TTT
1 TC-ATTGATGCAATCCAATAGGGA-AGGTCTCAATC
624869 TCATTGATGCAATCCAATAGGGAAGGTCTCAATC
1 TCATTGATGCAATCCAATAGGGAAGGTCTCAATC
624903 TCATT
1 TCATT
624908 CCATGCACCA
Statistics
Matches: 47, Mismatches: 12, Indels: 18
0.61 0.16 0.23
Matches are distributed among these distances:
28 3 0.06
29 10 0.21
30 3 0.06
31 5 0.11
32 5 0.11
33 3 0.06
34 15 0.32
35 3 0.06
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (34 bp):
TCATTGATGCAATCCAATAGGGAAGGTCTCAATC
Found at i:631474 original size:72 final size:72
Alignment explanation
Indices: 631357--631500 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
631347 AAGTGTCAGA
631357 GTTTGTTTCTCGGTGTCAAGTGTATCAGTCGAGTAAGGCTGAACAATAGGCTCCCTCAGGGTTAC
1 GTTTGTTTCTCGGTGTCAAGTGTATCAGTCGAGTAAGGCTGAACAATAGGCTCCCTCAGGGTTAC
631422 TTCATCC
66 TTCATCC
631429 GTTTGTTTCTCGGTGTCAAGTGTATCAGTCGAGTAAGGCTGAACAATAGGCTCCCTCAGGGTTAC
1 GTTTGTTTCTCGGTGTCAAGTGTATCAGTCGAGTAAGGCTGAACAATAGGCTCCCTCAGGGTTAC
631494 TTCATCC
66 TTCATCC
631501 CATTCAGATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (72 bp):
GTTTGTTTCTCGGTGTCAAGTGTATCAGTCGAGTAAGGCTGAACAATAGGCTCCCTCAGGGTTAC
TTCATCC
Found at i:634178 original size:76 final size:76
Alignment explanation
Indices: 634052--634203 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
634042 TTCCATACTC
634052 TTTTTCCTCATTCTTCCTTGTCTTCTTCTTCTTTTTCCTATATTTCTTGATTCATCCTCTCCAAG
1 TTTTTCCTCATTCTTCCTTGTCTTCTTCTTCTTTTTCCTATATTTCTTGATTCATCCTCTCCAAG
634117 AACCAAGAAAA
66 AACCAAGAAAA
634128 TTTTTCCTCATTCTTCCTTGTCTTCTTCTTCTTTTTCCTATATTTCTTGATTCATCCTCTCCAAG
1 TTTTTCCTCATTCTTCCTTGTCTTCTTCTTCTTTTTCCTATATTTCTTGATTCATCCTCTCCAAG
634193 AACCAAGAAAA
66 AACCAAGAAAA
634204 ATTGGAACTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (76 bp):
TTTTTCCTCATTCTTCCTTGTCTTCTTCTTCTTTTTCCTATATTTCTTGATTCATCCTCTCCAAG
AACCAAGAAAA
Found at i:634983 original size:18 final size:18
Alignment explanation
Indices: 634960--635002 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
634950 TTTTAGTACT
634960 GATACCTAGGGTGGTATC
1 GATACCTAGGGTGGTATC
634978 GATACCTAGGGTGGTATC
1 GATACCTAGGGTGGTATC
634996 GATACCT
1 GATACCT
635003 GTACTGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
GATACCTAGGGTGGTATC
Found at i:635108 original size:20 final size:21
Alignment explanation
Indices: 635079--635122 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
635069 TATCAATACC
635079 AGGGGCCAGTATCGATACT-A
1 AGGGGCCAGTATCGATACTGA
*
635099 AGGGGTCAGTATCGATACTGA
1 AGGGGCCAGTATCGATACTGA
635120 AGG
1 AGG
635123 CTTATTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.20
Consensus pattern (21 bp):
AGGGGCCAGTATCGATACTGA
Found at i:638644 original size:71 final size:73
Alignment explanation
Indices: 638510--638654 Score: 276
Period size: 71 Copynumber: 2.0 Consensus size: 73
638500 AGAATCATCA
638510 TCAACAGTAAACCCATACCAAATATTTTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTT
1 TCAACAGTAAACCCATACCAAATATTTTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTT
638575 TAATATTT
66 TAATATTT
638583 TCAACAGTAAACCCATACC-AATATTTTGAAAAATCAGAC-TTTGTCATATTGGGATCCAATTTT
1 TCAACAGTAAACCCATACCAAATATTTTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTT
638646 TAATATTT
66 TAATATTT
638654 T
1 T
638655 GCAGGTTGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 33 0.46
72 20 0.28
73 19 0.26
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (73 bp):
TCAACAGTAAACCCATACCAAATATTTTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTT
TAATATTT
Found at i:638665 original size:52 final size:53
Alignment explanation
Indices: 638608--638712 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
638598 TACCAATATT
638608 TTGAAAAATCAGAC-TTTGTCATATTGGGATCCAATTTTTAATATTTTGCAGG
1 TTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTTTAATATTTTGCAGG
638660 TTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTTTAATATTTTGCAGG
1 TTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTTTAATATTTTGCAGG
638713 GAAATCGTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 14 0.27
53 38 0.73
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (53 bp):
TTGAAAAATCAGACTTTTGTCATATTGGGATCCAATTTTTAATATTTTGCAGG
Found at i:649136 original size:48 final size:49
Alignment explanation
Indices: 649061--649158 Score: 189
Period size: 48 Copynumber: 2.0 Consensus size: 49
649051 AATTCCTAAA
649061 TGTTCGAATAATATTATATGGATCCTCTTGTTTGTTCCATTTTGAAATG
1 TGTTCGAATAATATTATATGGATCCTCTTGTTTGTTCCATTTTGAAATG
649110 TGTTCGAATAATA-TATATGGATCCTCTTGTTTGTTCCATTTTGAAATG
1 TGTTCGAATAATATTATATGGATCCTCTTGTTTGTTCCATTTTGAAATG
649158 T
1 T
649159 AAATGTTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 36 0.73
49 13 0.27
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (49 bp):
TGTTCGAATAATATTATATGGATCCTCTTGTTTGTTCCATTTTGAAATG
Found at i:659431 original size:39 final size:36
Alignment explanation
Indices: 659372--659481 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 36
659362 AAAAAAATAA
*
659372 AAAATAAAATAAAATAAAAAAGAGAGAGAAAG-AAAATT
1 AAAATAAAA-AAAATAAAAAA-AGA-AAAAAGAAAAATT
*
659410 AAAATTAAAAAAAATAAAAAAATGAAAAAAGATAAAAAT
1 AAAA-TAAAAAAAATAAAAAAA-GAAAAAAGA-AAAATT
* * *
659449 AAAATAAAAAAAAGAAAAAAAGAATAAACAAAA
1 AAAATAAAAAAAATAAAAAAAGAAAAAAGAAAA
659482 GGGGATCAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
36 3 0.05
37 13 0.21
38 33 0.52
39 14 0.22
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.12
Consensus pattern (36 bp):
AAAATAAAAAAAATAAAAAAAGAAAAAAGAAAAATT
Found at i:659481 original size:22 final size:22
Alignment explanation
Indices: 659358--659482 Score: 82
Period size: 21 Copynumber: 5.8 Consensus size: 22
659348 ATTTTGCTCG
*
659358 AATAAAA-AAAATAAAAAAT-AA
1 AATAAAATAAAA-AAAAGATAAA
* * *
659379 AATAAAATAAAAAAGAGAGAGA
1 AATAAAATAAAAAAAAGATAAA
* **
659401 AAGAAAATTAAAATTAA-A-AAA
1 AATAAAA-TAAAAAAAAGATAAA
*
659422 AATAAAAAAATGAAAAAAGATAAA
1 AATAAAATAA--AAAAAAGATAAA
659446 AATAAAATAAAAAAAAGA-AAA
1 AATAAAATAAAAAAAAGATAAA
* *
659467 AA-AGAATAAACAAAAG
1 AATAAAATAAAAAAAAG
659483 GGGATCAAGA
Statistics
Matches: 81, Mismatches: 16, Indels: 15
0.72 0.14 0.13
Matches are distributed among these distances:
20 14 0.17
21 24 0.30
22 24 0.30
23 7 0.09
24 12 0.15
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.12
Consensus pattern (22 bp):
AATAAAATAAAAAAAAGATAAA
Found at i:659481 original size:29 final size:29
Alignment explanation
Indices: 659415--659481 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
659405 AAATTAAAAT
*
659415 TAAAAAAAATAAAAAAATGAAAAAAGATA
1 TAAAAAAAATAAAAAAAAGAAAAAAGATA
659444 -AAAATAAAATAAAAAAAAGAAAAAAAGA-A
1 TAAAA-AAAATAAAAAAAAG-AAAAAAGATA
*
659473 TAAACAAAA
1 TAAAAAAAA
659482 GGGGATCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.12
29 18 0.55
30 11 0.33
ACGTcount: A:0.82, C:0.01, G:0.06, T:0.10
Consensus pattern (29 bp):
TAAAAAAAATAAAAAAAAGAAAAAAGATA
Found at i:660981 original size:134 final size:131
Alignment explanation
Indices: 660692--660990 Score: 384
Period size: 131 Copynumber: 2.2 Consensus size: 131
660682 ACAAATCGAA
* * * * * *
660692 CTCGATTCAATATTCCCTGAGCAACAGTGGAATGAATCAACATCCTCAGATCTGATTTTTCTCTC
1 CTCGATTCAATCTTCCCTAAG-AACAGTGGAATGAATCAACATCCCCAGATCTGAATTTCCCCTC
*
660757 AAGAAAAAGCAGAACAGGTCCATCTCTTTCAAGATTTGATATTCCCTGAATAGTGGAACAAGTCT
65 AAGAAAAAGCAGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAATAGTGGAACAAGTCT
660822 AC
130 AC
* * * * *
660824 ATTGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAACGTCCCCAGATCT-AATTTCCCCTC
1 CTCGATTCAATCTTCCCT-AAGAACAGTGGAATGAATCAACATCCCCAGATCTGAATTTCCCCTC
* * * *
660888 AAGAAGAAGCGGAATAGATTCATCTCTTTCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAG
65 AAGAAAAAGCAGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGA---ATAGTGGAACAAG
660953 TCTAC
127 TCTAC
*
660958 CTCGATTCAATCTTCCCTAAAGAACAGTAGAAT
1 CTCGATTCAATCTTCCCT-AAGAACAGTGGAAT
660991 AAGTCAATGT
Statistics
Matches: 141, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
131 52 0.37
132 42 0.30
133 2 0.01
134 45 0.32
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (131 bp):
CTCGATTCAATCTTCCCTAAGAACAGTGGAATGAATCAACATCCCCAGATCTGAATTTCCCCTCA
AGAAAAAGCAGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAATAGTGGAACAAGTCTA
C
Found at i:663256 original size:17 final size:18
Alignment explanation
Indices: 663226--663265 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
663216 AACGCATATC
*
663226 ATTTTTTCTTTTAAAATT
1 ATTTTTTCTCTTAAAATT
663244 ATTTTTT-TCTTAAAATT
1 ATTTTTTCTCTTAAAATT
663261 ATTTT
1 ATTTT
663266 AAAGGATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTCTCTTAAAATT
Found at i:669613 original size:44 final size:43
Alignment explanation
Indices: 669535--669652 Score: 186
Period size: 44 Copynumber: 2.7 Consensus size: 43
669525 AAATAAGCTT
*
669535 AGCTTATGGA-ATAATGGCAATATATTGGTAAAATAAGCTTACG
1 AGCTTATGGATA-AATGGTAATATATTGGTAAAATAAGCTTACG
669578 AGCTTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACG
1 AGCTTATGGATAAATGGTAA-TATATTGGTAAAATAAGCTTACG
669622 AGCTTATGGATTAAATGGTAAT-TATTGGTAA
1 AGCTTATGGA-TAAATGGTAATATATTGGTAA
669653 GAAAGTTGTA
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
43 26 0.37
44 35 0.49
45 10 0.14
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (43 bp):
AGCTTATGGATAAATGGTAATATATTGGTAAAATAAGCTTACG
Found at i:675246 original size:14 final size:14
Alignment explanation
Indices: 675227--675271 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
675217 CTAGAAACGC
675227 ATATACTTATAGAT
1 ATATACTTATAGAT
675241 ATATACTTATAGAT
1 ATATACTTATAGAT
*
675255 ATATACTTATATAT
1 ATATACTTATAGAT
675269 ATA
1 ATA
675272 ATGAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
ATATACTTATAGAT
Found at i:678972 original size:29 final size:29
Alignment explanation
Indices: 678939--679112 Score: 240
Period size: 29 Copynumber: 6.0 Consensus size: 29
678929 TCCATTATTC
**
678939 TTTACTCAACAGTGTTTAATTGTTCATCT
1 TTTACTCAACAGTGTTTAACCGTTCATCT
* *
678968 TTTACTCAATAGTGCTTAACCGTTCATCT
1 TTTACTCAACAGTGTTTAACCGTTCATCT
* *
678997 TTTACTCAATAGTGCTTAACCGTTCATCT
1 TTTACTCAACAGTGTTTAACCGTTCATCT
* * *
679026 TTTACTCAATAGAGTTTAACTGTTCATCT
1 TTTACTCAACAGTGTTTAACCGTTCATCT
* *
679055 TTTACTCAACTGTATTTAACCGTTCATCT
1 TTTACTCAACAGTGTTTAACCGTTCATCT
*
679084 TTTACTCAACAGTATTTAACCGTTCATCT
1 TTTACTCAACAGTGTTTAACCGTTCATCT
679113 AATTGGGATA
Statistics
Matches: 132, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 132 1.00
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTACTCAACAGTGTTTAACCGTTCATCT
Found at i:679216 original size:81 final size:81
Alignment explanation
Indices: 679081--679235 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 81
679071 TAACCGTTCA
* * * * *
679081 TCTTTTACTCAACAGTATTTAACCGTTCATCTAATTGGGATAATTGACACCTTTCTGT-CAAATA
1 TCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATCGAAACCTTTCT-TCCAAATA
*
679145 CACAGTTAGGCCATTAT
65 CACAGCTAGGCCATTAT
* *
679162 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATGAA-CGAAACCTTTCTTCCAAATG
1 TCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCAT-AATCGAAACCTTTCTTCCAAATA
679226 CACAGCTAGG
65 CACAGCTAGG
679236 ACTCAAAGGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.02
81 61 0.95
82 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATCGAAACCTTTCTTCCAAATAC
ACAGCTAGGCCATTAT
Found at i:679292 original size:68 final size:68
Alignment explanation
Indices: 679187--679846 Score: 916
Period size: 68 Copynumber: 9.8 Consensus size: 68
679177 TATTTAACCA
* * * * * * *
679187 TTCATCTAACTGGCATGAACGAAACCTTTCT-TCCAAATGCACAGCTAGGACTCAAAGGCAGTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGT-CAAATCCACAGTTAGGCCTCAAAGGCACTTA
679251 GCCT
65 GCCT
* * * * *
679255 TTCATCTAACTGGCATAAATGACATCTTCCTGTCAAATGCACAGCTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679320 CCT
66 CCT
* * * *
679323 TTCATCTAACTGACATAAATGACACATTTATGTCAAA--CACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679386 CCT
66 CCT
* * * *
679389 TTCATATAACTGGCATAAATGACACCTTTATTTCAAATCCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679454 CCT
66 CCT
* *
679457 TTCATATAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679522 CCT
66 CCT
* *
679525 TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATCCACAGTAAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679590 CCT
66 CCT
* * * * *
679593 TTCATCTAACTGGCATAAATGACACATTTCTATAAAATGCACAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679658 CCT
66 CCT
* * * *
679661 TTCATCTAACTGGCATAAATGACACTTTTATGTCAAATACACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679726 CCT
66 CCT
* * * *
679729 TTCATATAACTGGCATAAATGACACCTTTATTTCAAATCCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
679794 CCT
66 CCT
* * *
679797 TTCATATAACTGGCATAAATGATACATTTCTGTCAAA--CACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCT
679847 ATTAATCTTT
Statistics
Matches: 535, Mismatches: 54, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
66 72 0.13
68 462 0.86
69 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:680151 original size:55 final size:55
Alignment explanation
Indices: 680022--680173 Score: 170
Period size: 55 Copynumber: 2.8 Consensus size: 55
680012 ACATATATTT
*
680022 CCCATACGA-AAATTCATACACTTGGA-ATGAATTTCTTA-TTTCACACACATAGTG
1 CCCATAC-ATAAATTCATACACTT-AATATGAATTTCTTAGTTTCACACACATAGTG
* * *
680076 ACCAAACATAAATTTATACACTTAATATGAATTTCTTAGGTTTGCACACA-A-AGTG
1 CCCATACATAAATTCATACACTTAATATGAATTTCTTA-GTTT-CACACACATAGTG
* *
680131 CCCATACATAAATTCGTACACTTAATATTAATTTCTTAAGTTT
1 CCCATACATAAATTCATACACTTAATATGAATTTCTT-AGTTT
680174 TTGTACACTT
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
53 2 0.02
54 30 0.36
55 40 0.48
56 5 0.06
57 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (55 bp):
CCCATACATAAATTCATACACTTAATATGAATTTCTTAGTTTCACACACATAGTG
Found at i:682038 original size:623 final size:630
Alignment explanation
Indices: 680812--682064 Score: 1981
Period size: 623 Copynumber: 2.0 Consensus size: 630
680802 ATACAATACT
* *
680812 ATCAAACTCTTCTTTAACTATCCATACTAACATTCCTTCATTTTAATACTTAAAACATCTAGTAC
1 ATCAAACTCTTCTTTAACAATCCATACTAACATTCCTTCATTTTAATACATAAAACATCTAGTAC
680877 CCCTCAAGATCATTGGATTCTAAGAATCACACAAAAGTTCTAACTTGTTTTAAACTCATCCAATG
66 CCCTCAAGATCATTGGATTCTAAGAATCACACAAAAGTTCTAACTTGTTTTAAACTCATCCAATG
* *
680942 CTTCTAATCTCTTATTTACTACTTTGACAAGTCAATTCTATCAATAAACATCAATAAACACTCAT
131 CTTCTAATCTCTTATTTACTACTTTGACAAGTCAATTATACCAATAAACATCAATAAACACTCA-
* * *
681007 ATATTAACATATCATTTAGAAACCTATTTTCTTAAATCTCTAATATTTCATCCATTTCATAGTTT
195 ATATCAACATATCATTTAGAAACCCATTTTCTTAAATCTATAATATTTCATCCATTTCATAGTTT
* * * * *
681072 TGATCCCCTTTAATCCTTCCTTAAGCTTATATTATACTCAATGCTTTAAAAGCCACCCAAAAATG
260 TGATCCCCTTTAATCCTTACTTAAGCTTATATTAAACTCAATACTTTAAAAGACACCCAAAAACG
* *
681137 ATGGAATAAACTAGTAATTGAAAACTCACCTTTAGCTATGGAGGAGAGCTTTTCCACGGGAAGAA
325 AAGGAATAAACTAG--ATTGAAAACTCACCTTTAGCTATGGAGAAGAGCTTTTCCACGGGAAGAA
*
681202 AGAGAAGAAGAAAAGAGGATAACATTTGGTAACCTATTTTCCCTTTCCCCCTTTTACTTAATATC
388 AGAGAAGAAGAAAAGAGGATAACATTTGGTAACCTATTTTCCCCTTCCCCCTTTTACTTAATATC
681267 TTATTAAAAATAAAATTTAAATTCATTTTCCCTTTAAAGGACCAAAATAACCTCATAATCATCCA
453 TTATTAAAAATAAAATTTAAATTCATTTTCCCTTTAAAGGACCAAAATAACCTCATAATCATCCA
* * * *
681332 TTGATATAATTTAGTCTAAACCACTATTTCAAATCATTCTCAACTTTTATCAATTTGTTAAATAA
518 TTGATACAATTTACTATAAACCACTATTTCAAATCATTCTCAACTTTTATAAATTTGTTAAATAA
* *
681397 ATACTTATATTTTAAATTCTTTCAATAAAGTCATTATTTCCATATTGGG
583 ATACTGATATTTTAAATTCTTTCAATAAAGTCACTA-TTCCATATTGGG
681446 ATCAAACTCTTC-TTAACAATCCATACTAACATTCCTTCATTTTAATACATAAAACATCTAGTAC
1 ATCAAACTCTTCTTTAACAATCCATACTAACATTCCTTCATTTTAATACATAAAACATCTAGTAC
* * *
681510 CCCTCAAGATCATTGGATTTTAAGAATCATACCAAAATTTCTAACTTGTTTTTAAACTCATCCAA
66 CCCTCAAGATCATTGGATTCTAAGAATCACA-CAAAAGTTCTAACTTG-TTTTAAACTCATCCAA
*
681575 TGCTTCTAATCTCTTATTTACTACTTTGACAAGTTAATTATACCAATAAACATCAATAAACACTC
129 TGCTTCTAATCTCTTATTTACTACTTTGACAAGTCAATTATACCAATAAACATCAATAAACACTC
* *
681640 -ATATCAACATATCATTTTA-AAACCCATTTTCTTATATCTATAATATTTCCTCCATTTCATAG-
194 AATATCAACATATCA-TTTAGAAACCCATTTTCTTAAATCTATAATATTTCATCCATTTCATAGT
* *
681702 TTTGATCCCCTTTAATTCTTACTTAAGCTTATATTAAACTCAATACTTTAAAAGACACTCAAAAA
258 TTTGATCCCCTTTAATCCTTACTTAAGCTTATATTAAACTCAATACTTTAAAAGACACCCAAAAA
* *
681767 CGAAGGAATAAACTAG-TTGAAAACTCACCTTTAGCTATGGAGAAGAGTTTTTCCAC-GGAA-AG
323 CGAAGGAATAAACTAGATTGAAAACTCACCTTTAGCTATGGAGAAGAGCTTTTCCACGGGAAGAA
*
681829 AGA-AAGAA-AAAAGAGGATAACTTTTGGTAACCTATTTTCCCCTTCCCCC-TTTACTTAATATC
388 AGAGAAGAAGAAAAGAGGATAACATTTGGTAACCTATTTTCCCCTTCCCCCTTTTACTTAATATC
* ** *
681891 TTATT-AAAATAAATTTTAAATTCATTTTCCCTTTAAAGGACCAAAATGCCCTCATCATCATCCA
453 TTATTAAAAATAAAATTTAAATTCATTTTCCCTTTAAAGGACCAAAATAACCTCATAATCATCCA
* *
681955 TTGCTACAATTTACTATAAACCACTATTTCAAATCATTCTTAACTTTTATAAATTTGTTAAATAA
518 TTGATACAATTTACTATAAACCACTATTTCAAATCATTCTCAACTTTTATAAATTTGTTAAATAA
* * *
682020 ATCCTCGAT-TTTTAAATTCTTTTAATAAAGTCCCTATTCCATATT
583 ATACT-GATATTTTAAATTCTTTCAATAAAGTCACTATTCCATATT
682065 TAGGGTATTA
Statistics
Matches: 574, Mismatches: 41, Indels: 20
0.90 0.06 0.03
Matches are distributed among these distances:
622 9 0.02
623 142 0.25
624 20 0.03
625 39 0.07
626 5 0.01
627 4 0.01
628 4 0.01
629 38 0.07
632 73 0.13
633 131 0.23
634 31 0.05
635 78 0.14
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (630 bp):
ATCAAACTCTTCTTTAACAATCCATACTAACATTCCTTCATTTTAATACATAAAACATCTAGTAC
CCCTCAAGATCATTGGATTCTAAGAATCACACAAAAGTTCTAACTTGTTTTAAACTCATCCAATG
CTTCTAATCTCTTATTTACTACTTTGACAAGTCAATTATACCAATAAACATCAATAAACACTCAA
TATCAACATATCATTTAGAAACCCATTTTCTTAAATCTATAATATTTCATCCATTTCATAGTTTT
GATCCCCTTTAATCCTTACTTAAGCTTATATTAAACTCAATACTTTAAAAGACACCCAAAAACGA
AGGAATAAACTAGATTGAAAACTCACCTTTAGCTATGGAGAAGAGCTTTTCCACGGGAAGAAAGA
GAAGAAGAAAAGAGGATAACATTTGGTAACCTATTTTCCCCTTCCCCCTTTTACTTAATATCTTA
TTAAAAATAAAATTTAAATTCATTTTCCCTTTAAAGGACCAAAATAACCTCATAATCATCCATTG
ATACAATTTACTATAAACCACTATTTCAAATCATTCTCAACTTTTATAAATTTGTTAAATAAATA
CTGATATTTTAAATTCTTTCAATAAAGTCACTATTCCATATTGGG
Found at i:685300 original size:2 final size:2
Alignment explanation
Indices: 685293--685342 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
685283 TACATTATCC
685293 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
685335 AT AT AT AT
1 AT AT AT AT
685343 CATCCCTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:685512 original size:29 final size:29
Alignment explanation
Indices: 685479--685713 Score: 371
Period size: 29 Copynumber: 8.1 Consensus size: 29
685469 AGTCCATTAT
* **
685479 TCTTTTACTCAACAGTGTTTAACTATTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
685508 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
685537 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
685566 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
685595 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
685624 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
685653 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
* *
685682 TCTTTTACTCAATAGTATTTAACAGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
685711 TCT
1 TCT
685714 AACTGGGATA
Statistics
Matches: 199, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 199 1.00
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTATTTAACCGTTCA
Found at i:685900 original size:68 final size:68
Alignment explanation
Indices: 685786--686113 Score: 396
Period size: 68 Copynumber: 4.9 Consensus size: 68
685776 TATTAAATCG
* * ** * *
685786 TTCATCTAACTGTCATAAATGAAACCTTTATACCAAATGCACAGTTAGGCCTCAAAAGCATTTAG
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
685851 CCT
66 CCT
* * *
685854 TTCATCGAACTGGCATAAATGAAACCTTTATGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
685919 CCT
66 CCT
* * * * *
685922 TTCATCTAACTGGCATAAAT----CATTTCTATCAAATGCAAAGTTATGCCTCAAAGGCAATTAG
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
685983 CTT
66 CCT
* * * * * * *
685986 TTCATCTAACTGACATAAAT-AACACATTTCTGTCGAATCCATAGTTAGGCCTTAAAGGTACTTA
1 TTCATCTAACTGGCATAAATGAA-ACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
686050 GCCT
65 GCCT
* *
686054 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCA
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCA
686114 TGTCGCTACA
Statistics
Matches: 222, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
64 56 0.25
68 165 0.74
69 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:686029 original size:132 final size:134
Alignment explanation
Indices: 685786--686113 Score: 419
Period size: 132 Copynumber: 2.4 Consensus size: 134
685776 TATTAAATCG
* * * * * *
685786 TTCATCTAACTGTCATAAATGAAACCTTTATACCAAATGCACAGTTAGGCCTCAAAAGCATTTAG
1 TTCATCTAACTGGCATAAAT-ACA-CTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAATTAG
* * *
685851 CCTTTCATCGAACTGGCATAAATGAAACCTTTATGTCAAATGCATAGTTAGGCCTCAAAGGCACT
64 CCTTTCATCGAACTGACATAAATGAAACATTTATGTCAAATCCATAGTTAGGCCTCAAAGGCACT
685916 TAGCCT
129 TAGCCT
* * *
685922 TTCATCTAACTGGCATAAAT-CA-TTTCTATCAAATGCAAAGTTATGCCTCAAAGGCAATTAGCT
1 TTCATCTAACTGGCATAAATACACTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAATTAGCC
* * * * *
685985 TTTCATCTAACTGACATAAAT-AACACATTTCTGTCGAATCCATAGTTAGGCCTTAAAGGTACTT
66 TTTCATCGAACTGACATAAATGAA-ACATTTATGTCAAATCCATAGTTAGGCCTCAAAGGCACTT
686049 AGCCT
130 AGCCT
* *
686054 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCA
1 TTCATCTAACTGGCATAAAT-ACA-CTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCA
686114 TGTCGCTACA
Statistics
Matches: 166, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
131 2 0.01
132 112 0.67
134 3 0.02
136 49 0.30
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (134 bp):
TTCATCTAACTGGCATAAATACACTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAATTAGCC
TTTCATCGAACTGACATAAATGAAACATTTATGTCAAATCCATAGTTAGGCCTCAAAGGCACTTA
GCCT
Found at i:689097 original size:21 final size:21
Alignment explanation
Indices: 689073--689135 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
689063 TACCTGATTG
689073 ACTTCATAATTGTTAATCAAA
1 ACTTCATAATTGTTAATCAAA
* * * * *
689094 ACTTGA-ATTTTTTTATCATTA
1 ACTTCATAATTGTTAATCA-AA
*
689115 ACTTCATCATTGTTAATCAAA
1 ACTTCATAATTGTTAATCAAA
689136 GCCCAAACCA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (21 bp):
ACTTCATAATTGTTAATCAAA
Found at i:690207 original size:30 final size:30
Alignment explanation
Indices: 690172--690262 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
690162 TATTAGAGTG
690172 TGCCTAAAGACCAATCATATGATGATTGTA
1 TGCCTAAAGACCAATCATATGATGATTGTA
690202 TGCCTAAAGACCAATCATATGATGATTGTA
1 TGCCTAAAGACCAATCATATGATGATTGTA
*
690232 TGCCTAAAGATCAATCATATGATGATTGTA
1 TGCCTAAAGACCAATCATATGATGATTGTA
690262 T
1 T
690263 TGACATATTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (30 bp):
TGCCTAAAGACCAATCATATGATGATTGTA
Found at i:691347 original size:3 final size:3
Alignment explanation
Indices: 691339--691363 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
691329 GAATCAACCC
691339 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
691364 ATTTGTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:695550 original size:23 final size:23
Alignment explanation
Indices: 695511--695557 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
695501 GACGATCGGT
*
695511 TTTTTTACCGGATAAAAAACCGG
1 TTTTTTACCGGAAAAAAAACCGG
*
695534 TTTTTTATCC-GAAAAAAATCCGG
1 TTTTTTA-CCGGAAAAAAAACCGG
695557 T
1 T
695558 CCGGGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (23 bp):
TTTTTTACCGGAAAAAAAACCGG
Found at i:698211 original size:13 final size:13
Alignment explanation
Indices: 698175--698213 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
698165 GTCTACATGC
698175 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
698188 AATGAGTGTCATA
1 AATGCGCGTCATA
698201 AATGCGCGTCATA
1 AATGCGCGTCATA
698214 GATTTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:700129 original size:2 final size:2
Alignment explanation
Indices: 700122--700150 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
700112 CTGCAAACGC
700122 AT 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 AT A
700151 ATGAAATTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:707164 original size:38 final size:36
Alignment explanation
Indices: 707092--707164 Score: 85
Period size: 38 Copynumber: 2.0 Consensus size: 36
707082 TAAAAAATAA
**
707092 ATGTTATAAATATATTTTTATAATATTTTATAATTT
1 ATGTTATAAATATATTTTTATAATACATTATAATTT
*
707128 ATGTTATAATTAATTATTTTTATAAATACATT-TAATT
1 ATGTTATAAAT-A-TATTTTTAT-AATACATTATAATT
707165 AGTTTCAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 10 0.32
37 1 0.03
38 14 0.45
39 6 0.19
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (36 bp):
ATGTTATAAATATATTTTTATAATACATTATAATTT
Found at i:708769 original size:8 final size:8
Alignment explanation
Indices: 708756--708795 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
708746 GATGTTTGAT
708756 TTATTTTA
1 TTATTTTA
708764 TTATTTTA
1 TTATTTTA
708772 TTATTAATT-
1 TTATT--TTA
708781 TTATTTTA
1 TTATTTTA
708789 TTATTTT
1 TTATTTT
708796 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 2 0.07
8 20 0.69
9 5 0.17
10 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Done.