Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 29 of 190
Found at i:8251332 original size:2 final size:2
Alignment explanation
Indices: 8251327--8251374 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
8251317 AAATAGTGCT
8251327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8251369 TA TA TA
1 TA TA TA
8251375 ATGCTCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8251436 original size:8 final size:8
Alignment explanation
Indices: 8251423--8251447 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
8251413 CTTAAATATG
8251423 TATTTTAT
1 TATTTTAT
8251431 TATTTTAT
1 TATTTTAT
8251439 TATTTTAT
1 TATTTTAT
8251447 T
1 T
8251448 TAAAATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:8251800 original size:2 final size:2
Alignment explanation
Indices: 8251793--8251840 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
8251783 TTGACAAAGT
8251793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8251835 TA TA TA
1 TA TA TA
8251841 CTTTTACTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8258576 original size:16 final size:17
Alignment explanation
Indices: 8258555--8258586 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8258545 AAATATGCAA
8258555 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
8258571 TCACATAACTTCATAT
1 TCACATAACTTCATAT
8258587 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:8258845 original size:41 final size:43
Alignment explanation
Indices: 8258787--8258911 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 43
8258777 TAATTACGTA
*
8258787 TCGATGCCACTGTCCCAGACAGGGTCTTACACAAAT-CA-AA-
1 TCGATGCCAATGTCCCAGACAGGGTCTTACACAAATACACAAG
* * **
8258827 TACGATGTCAATGTCCCAGACATGGTCTTACACGTATACACAAG
1 T-CGATGCCAATGTCCCAGACAGGGTCTTACACAAATACACAAG
*
8258871 TCGATGCCAACGTCCCAGAC-GTGGTCTTACACGAAAATACA
1 TCGATGCCAATGTCCCAGACAG-GGTCTTACAC--AAATACA
8258912 TATCGAAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 30 0.44
42 2 0.03
43 29 0.43
44 1 0.01
45 5 0.07
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
TCGATGCCAATGTCCCAGACAGGGTCTTACACAAATACACAAG
Found at i:8258889 original size:43 final size:41
Alignment explanation
Indices: 8258747--8258903 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 41
8258737 GGCTCGTACA
* * **
8258747 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATTACGTATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-A-TACAAATCG
* **
8258790 ATGCC-ACTGTCCCAGACAGGGTCTTACACAAAT-CAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTATACAAAT-CG
* *
8258831 ATGTCAATGTCCCAGACATGGTCTTACACGTATACACAAGTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTATACA-AA-TCG
*
8258874 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
8258904 AAAATACATA
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
40 3 0.03
41 29 0.31
42 6 0.06
43 54 0.58
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTATACAAATCG
Found at i:8265340 original size:22 final size:22
Alignment explanation
Indices: 8265298--8265354 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
8265288 CCCTTATTTC
*
8265298 ATTTTCACATTTATTTATTTATT
1 ATTTT-ACTTTTATTTATTTATT
8265321 ATTTT-CTTTTATTGTATTTATT
1 ATTTTACTTTTATT-TATTTATT
8265343 ATTTTACTTTTA
1 ATTTTACTTTTA
8265355 CTACTCCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 7 0.23
22 13 0.42
23 11 0.35
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (22 bp):
ATTTTACTTTTATTTATTTATT
Found at i:8269356 original size:29 final size:30
Alignment explanation
Indices: 8269322--8269391 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
8269312 TTTTTAAATC
*
8269322 ATTTTTAAATATATATATTT-AGTCACTTA
1 ATTTTTAAAAATATATATTTGAGTCACTTA
*
8269351 ATTTTTAAAAATATTTATTTGAGTCACTTA
1 ATTTTTAAAAATATATATTTGAGTCACTTA
*
8269381 A-TTCTAAAAAT
1 ATTTTTAAAAAT
8269392 TTCACAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (30 bp):
ATTTTTAAAAATATATATTTGAGTCACTTA
Found at i:8270419 original size:2 final size:2
Alignment explanation
Indices: 8270412--8270438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8270402 TTCTATCTAT
8270412 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8270439 TANNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8274433 original size:19 final size:20
Alignment explanation
Indices: 8274385--8274438 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
8274375 CCCAAAATTT
* *
8274385 AGGTTTAGGGTTTGATGTTCG
1 AGGTTTAAGGTTT-AAGTTCG
*
8274406 AGATTTAAGGTTTAAGTTCG
1 AGGTTTAAGGTTTAAGTTCG
8274426 -GGTTTAAGGTTTA
1 AGGTTTAAGGTTTA
8274439 TTGTTTGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 12 0.41
20 6 0.21
21 11 0.38
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.43
Consensus pattern (20 bp):
AGGTTTAAGGTTTAAGTTCG
Found at i:8274997 original size:91 final size:91
Alignment explanation
Indices: 8274849--8275101 Score: 337
Period size: 90 Copynumber: 2.8 Consensus size: 91
8274839 ATGTCACATT
* * * *
8274849 TGGTACCTATACATTTATAAAATGTCCAATGTGATACTTGAACTATCAATTTATGTATTATTTGG
1 TGGTACCTATAC-TTT-GAAAATGTCCAATGTGGTACATGAACTATCAATTTGTGTATTATTTGG
*
8274914 TACTTGTACTTTCATAAAATGTCTAATA
64 TACTTGTACTTTCATAAAATGTCCAATA
8274942 TGGTACCTATACTTTGAAAATGTCCAATGTGGTACATGAACTATCAATTTGTGTATT-TTTGGTA
1 TGGTACCTATACTTTGAAAATGTCCAATGTGGTACATGAACTATCAATTTGTGTATTATTTGGTA
* * *
8275006 CATGTAGTTTCATAAAATGTCCAATG
66 CTTGTACTTTCATAAAATGTCCAATA
* ** * * **
8275032 TAGTAATTATACTTTGAAAATGTTCAATGTGGTACATGAACTATTAACCTGTGTATTATTATGGT
1 TGGTACCTATACTTTGAAAATGTCCAATGTGGTACATGAACTATCAATTTGTGTATTATT-TGGT
8275097 ACTTG
65 ACTTG
8275102 GAGTTAACAC
Statistics
Matches: 142, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
90 79 0.56
91 40 0.28
92 11 0.08
93 12 0.08
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (91 bp):
TGGTACCTATACTTTGAAAATGTCCAATGTGGTACATGAACTATCAATTTGTGTATTATTTGGTA
CTTGTACTTTCATAAAATGTCCAATA
Found at i:8275677 original size:29 final size:29
Alignment explanation
Indices: 8275632--8275741 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 29
8275622 TAGGTATCAT
* * *
8275632 ATTGAACATTTTCAAAGTATAAGTACCAC
1 ATTGGACATTTTTAAAGTACAAGTACCAC
8275661 ATTGGACATTTTTAAAGTACAAGTACCAC
1 ATTGGACATTTTTAAAGTACAAGTACCAC
* * * *
8275690 ATTAGACGTTTTATAAAAGTGCAAGGACCAC
1 ATTGGACATTTT-T-AAAGTACAAGTACCAC
*
8275721 ATTTGACATTTTATTAAAGTA
1 ATTGGACA-TTT-TTAAAGTA
8275742 TAGGTACTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
29 36 0.54
30 1 0.01
31 25 0.37
32 4 0.06
33 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (29 bp):
ATTGGACATTTTTAAAGTACAAGTACCAC
Found at i:8280298 original size:22 final size:21
Alignment explanation
Indices: 8280267--8280308 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8280257 TTTTTGTTAT
8280267 TAAATTTAATTATAAA-ATATG
1 TAAATTTAA-TATAAATATATG
8280288 TAAATATTAATATAAATATAT
1 TAAAT-TTAATATAAATATAT
8280309 AATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATTTAATATAAATATATG
Found at i:8280317 original size:20 final size:21
Alignment explanation
Indices: 8280267--8280318 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
8280257 TTTTTGTTAT
*
8280267 TAAA-TTTAATTATAAAATATG
1 TAAATTTTAA-TATAAAATATA
*
8280288 TAAATATTAATAT-AAATATA
1 TAAATTTTAATATAAAATATA
*
8280308 TAATTTTTAAT
1 TAAATTTTAAT
8280319 CTTTTATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 15 0.58
21 7 0.27
22 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:8289607 original size:22 final size:22
Alignment explanation
Indices: 8289565--8289608 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
8289555 TATCTAAATT
*
8289565 ATAAATATTTTTAATATTTAAA
1 ATAAATATTTTTAATAATTAAA
*
8289587 ATAAA-ATTTTGTTATAATTAAA
1 ATAAATATTTT-TAATAATTAAA
8289609 TGATTATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAAATATTTTTAATAATTAAA
Found at i:8292076 original size:15 final size:17
Alignment explanation
Indices: 8292047--8292079 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
8292037 GAAGTACTGA
8292047 ATTTTTTTGTAATTTTT
1 ATTTTTTTGTAATTTTT
8292064 ATTTTTTT-T-ATTTTT
1 ATTTTTTTGTAATTTTT
8292079 A
1 A
8292080 AAATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
ATTTTTTTGTAATTTTT
Found at i:8293081 original size:22 final size:22
Alignment explanation
Indices: 8293055--8293096 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8293045 GAGAAAAACA
*
8293055 AGAAAAATTAGATAAAAAGAGG
1 AGAAAAATTAGAGAAAAAGAGG
*
8293077 AGAAAAATTAGGGAAAAAGA
1 AGAAAAATTAGAGAAAAAGA
8293097 ATGGCAGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (22 bp):
AGAAAAATTAGAGAAAAAGAGG
Found at i:8293199 original size:13 final size:13
Alignment explanation
Indices: 8293181--8293205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8293171 TGTTAGATAC
8293181 TTAGACTTTAGTT
1 TTAGACTTTAGTT
8293194 TTAGACTTTAGT
1 TTAGACTTTAGT
8293206 AAATTAGGTT
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:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
TTAGACTTTAGTT
Found at i:8293266 original size:40 final size:38
Alignment explanation
Indices: 8293212--8293305 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 38
8293202 TAGTAAATTA
*
8293212 GGTTGGTAATTGGGTAGTCTTTTAATTTTAGTTTTATTG
1 GGTTGGTAATTGGGTAGGC-TTTAATTTTAGTTTTATTG
*
8293251 GGTTGCGTAATTGGGTAGGCTTTAGTTTTAGTTTTATTG
1 GGTTG-GTAATTGGGTAGGCTTTAATTTTAGTTTTATTG
8293290 GGTTGGGTAATTGGGT
1 GGTT-GGTAATTGGGT
8293306 CGGGTTGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 37 0.73
40 14 0.27
ACGTcount: A:0.16, C:0.03, G:0.32, T:0.49
Consensus pattern (38 bp):
GGTTGGTAATTGGGTAGGCTTTAATTTTAGTTTTATTG
Found at i:8295892 original size:14 final size:14
Alignment explanation
Indices: 8295869--8295899 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8295859 ATACTTTCAG
8295869 AATATAGAATCAAT
1 AATATAGAATCAAT
*
8295883 AATATGGAATCAAT
1 AATATAGAATCAAT
8295897 AAT
1 AAT
8295900 CCAACTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (14 bp):
AATATAGAATCAAT
Found at i:8305330 original size:42 final size:41
Alignment explanation
Indices: 8305186--8305349 Score: 185
Period size: 41 Copynumber: 4.0 Consensus size: 41
8305176 CTTTAAACAG
* * *
8305186 ATTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTG--ATT
1 ATTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAAATT
* * *
8305225 CAGTACACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGT
1 -A-TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAAAT-T
8305269 -TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATT
1 ATTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATT
8305309 ATTGCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAAT
1 ATT-CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAAT
8305350 GTTTCACTGG
Statistics
Matches: 109, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
40 4 0.04
41 65 0.60
42 37 0.34
43 2 0.02
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
ATTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATT
Found at i:8305344 original size:83 final size:82
Alignment explanation
Indices: 8305187--8305370 Score: 230
Period size: 83 Copynumber: 2.2 Consensus size: 82
8305177 TTTAAACAGA
*
8305187 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAG
1 TTCACTGGCA-TTAAGCCTGCTAGACGTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAG
*
8305251 ACATATAGTCTGAAATGT
65 ACATAAAGTCTGAAATGT
* * * *
8305269 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATT-ATTGCACCGGCA-TTAAGCCTGCT
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGCCTG--ATTCAGTACACCGGCACTT-AGCCTGCT
*
8305332 AGACGTAAAGTCTGAAATGT
63 AGACATAAAGTCTGAAATGT
* *
8305352 TTCACTGGCAATAAACCTG
1 TTCACTGGCATTAAGCCTG
8305371 ATAGGGACTG
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
81 2 0.02
82 31 0.35
83 52 0.59
84 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (82 bp):
TTCACTGGCATTAAGCCTGCTAGACGTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAGA
CATAAAGTCTGAAATGT
Found at i:8305547 original size:2 final size:2
Alignment explanation
Indices: 8305540--8305576 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8305530 ACATCCGAAC
8305540 AT AT AT AT 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 AT AT AT AT A
8305577 ACTTAATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8311232 original size:17 final size:18
Alignment explanation
Indices: 8311212--8311245 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8311202 TTGTTTAGAT
8311212 TAATT-AGAGTTTTATTA
1 TAATTGAGAGTTTTATTA
8311229 TAATTGAGAGTTTTATT
1 TAATTGAGAGTTTTATT
8311246 TGGATGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
TAATTGAGAGTTTTATTA
Found at i:8318445 original size:16 final size:17
Alignment explanation
Indices: 8318426--8318465 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
8318416 GGACAATGAT
*
8318426 GGAAAAGGACAA-AAAA
1 GGAAAAGGAAAAGAAAA
8318442 GGAAAAGGAAAAGAAAA
1 GGAAAAGGAAAAGAAAA
*
8318459 AGAAAAG
1 GGAAAAG
8318466 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (17 bp):
GGAAAAGGAAAAGAAAA
Found at i:8325171 original size:44 final size:44
Alignment explanation
Indices: 8325118--8325559 Score: 384
Period size: 44 Copynumber: 10.0 Consensus size: 44
8325108 TGACCTGCTA
* * * *
8325118 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTT
1 TCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* *** * *
8325162 TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAAATCTG-TT
1 TCTTCGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTT
* * *
8325206 TCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTATTT
1 TCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * *** * * *
8325250 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTA
1 TCTTCGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTT
* * *
8325295 TCTTTGATCTACTTCACGCCAGTAGATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * * * * *
8325339 TCTTCGATCTGCTTCGCCACCAGTATGA-GAAGGCAAGATCTGGTA
1 TCTTCGATCTACTTC-ACACCAGTA-CATGAAGACAAGATCTGTTT
* * * *
8325384 TCTTTGATCTACTTCACGCCAGTACATAAAGATAAGATCTGTTT
1 TCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * *** * * *
8325428 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTA
1 TCTTCGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTT
* *
8325473 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * * *
8325517 TCTTCGATTTGCTTCACCACCAGTACAGGAAGGCAAGATCTGT
1 TCTTCGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGT
8325560 ATATTCGATC
Statistics
Matches: 305, Mismatches: 85, Indels: 15
0.75 0.21 0.04
Matches are distributed among these distances:
43 19 0.06
44 145 0.48
45 139 0.46
46 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
Found at i:8325273 original size:133 final size:132
Alignment explanation
Indices: 8325014--8325595 Score: 488
Period size: 133 Copynumber: 4.4 Consensus size: 132
8325004 CTGCTTAGGG
* * * * *
8325014 AGATAAGATCTGTAATCTTCAATCTACTTCGCCACCAGTATGGGAAGATAAAATCTGTATATTTG
1 AGATAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGTATCTTTG
* * * * * * * * * *
8325079 ATCCACTTCGCTACCGATATAGGAAGACATGACCTGCTATCTTTGATCTACTTCACGCCAGTACA
66 ATCTACTTCAC-ACCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCACACCAGTACA
*
8325144 TGA
130 GGA
* * * * *
8325147 AGATAAGATCTATTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAAATCTGTTTCTTTG
1 AGATAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGTATCTTTG
* * * * **
8325212 ATCTACTTCACACCAATACATGAAGACAAGATCTATTTTCTTCGATCTGCTTCGCCACCAGTATG
66 ATCTACTTCACACCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTC-ACACCAGTACA
8325277 GGA
130 GGA
** * * * * * *
8325280 AGGCAAGATCTGGTATCTTTGATCTACTTCA-CGCCAGTA-GATGAAGACAAGATCTGTTTTCTT
1 AGATAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATG-GGAAGACAAAATCTG-TATCTT
* * * * * * * * *
8325343 CGATCTGCTTCGCCACCAGTATGA-GAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAGT
64 TGATCTACTTC-ACACCAATA-CATGAAGACAAGATCTGTTATCTTCGATCTACTTCACACCAGT
**
8325407 ACATAA
127 ACAGGA
* * * * *
8325413 AGATAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTTT
1 AGATAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAAATCT-GTATCTTT
* * * * *
8325478 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATTTGCTTCACCACCAGTAC
65 GATCTACTTCACACCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCA-CACCAGTAC
8325543 AGGA
129 AGGA
** * * * * * *
8325547 AGGCAAGATCTG-TATATTCGATCCACTTCGCTACCAATATAGGAAGACA
1 AGATAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGACA
8325596 GGATCTGCTG
Statistics
Matches: 349, Mismatches: 90, Indels: 20
0.76 0.20 0.04
Matches are distributed among these distances:
131 1 0.00
132 52 0.15
133 207 0.59
134 86 0.25
135 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (132 bp):
AGATAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAAATCTGTATCTTTG
ATCTACTTCACACCAATACATGAAGACAAGATCTGTTATCTTCGATCTACTTCACACCAGTACAG
GA
Found at i:8325467 original size:45 final size:44
Alignment explanation
Indices: 8325018--8325559 Score: 347
Period size: 44 Copynumber: 12.2 Consensus size: 44
8325008 TTAGGGAGAT
** * * *
8325018 AAGATCTGTAATCTTCAATCTACTTCGCCACCAGTATGGGAAGAT
1 AAGATCTGTTTTCTTCGATCTACTTC-CCACCAGTACGGGAAGAC
* * * * **
8325063 AAAATCTGTATAT-TT-GATCCACTTCGCTACC-GATATAGGAAGAC
1 AAGATCTGT-TTTCTTCGATCTACTTC-CCACCAG-TACGGGAAGAC
* * * * * * * ** *
8325107 ATGACCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGAT
1 AAGATCTGTTTTCTTCGATCTACTTCCCACCAGTACGGGAAGAC
* * * *
8325151 AAGATCTATTTTCTTCGATCTACTCCACCACCAGTATGGGGAGAC
1 AAGATCTGTTTTCTTCGATCTACTTC-CCACCAGTACGGGAAGAC
* * * * **
8325196 AAAATCTG-TTTCTTTGATCTACTTCACACCAATACATGAAGAC
1 AAGATCTGTTTTCTTCGATCTACTTCCCACCAGTACGGGAAGAC
* * * *
8325239 AAGATCTATTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGC
1 AAGATCTGTTTTCTTCGATCTACTTC-CCACCAGTACGGGAAGAC
* * * * * *
8325284 AAGATCTGGTATCTTTGATCTACTTCACGCCAGTA-GATGAAGAC
1 AAGATCTGTTTTCTTCGATCTACTTCCCACCAGTACG-GGAAGAC
* * * *
8325328 AAGATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGAGAAGGC
1 AAGATCTGTTTTCTTCGATCTACTTC-CCACCAGTACGGGAAGAC
* * * * * *** *
8325373 AAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATAAAGAT
1 AAGATCTGTTTTCTTCGATCTACTTCCCACCAGTACGGGAAGAC
* * *
8325417 AAGATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGC
1 AAGATCTGTTTTCTTCGATCTACTTC-CCACCAGTACGGGAAGAC
* * * * * **
8325462 AAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGAC
1 AAGATCTGTTTTCTTCGATCTACTTCCCACCAGTACGGGAAGAC
* * * *
8325506 AAGATCTGTTTTCTTCGATTTGCTTCACCACCAGTACAGGAAGGC
1 AAGATCTGTTTTCTTCGATCTACTTC-CCACCAGTACGGGAAGAC
8325551 AAGATCTGT
1 AAGATCTGT
8325560 ATATTCGATC
Statistics
Matches: 372, Mismatches: 112, Indels: 26
0.73 0.22 0.05
Matches are distributed among these distances:
43 23 0.06
44 187 0.50
45 159 0.43
46 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
AAGATCTGTTTTCTTCGATCTACTTCCCACCAGTACGGGAAGAC
Found at i:8325602 original size:89 final size:89
Alignment explanation
Indices: 8325116--8325575 Score: 699
Period size: 89 Copynumber: 5.2 Consensus size: 89
8325106 CATGACCTGC
* * * * *
8325116 TATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
* * *
8325181 CCAGTATGGGGAGACAAAATCT-G
66 CCAGTATGGGAAGGCAAGATCTGG
* * * *
8325204 TTTCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTATTTTCTTCGATCTGCTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
8325269 CCAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
*
8325293 TATCTTTGATCTACTTCACGCCAGTAGATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
*
8325358 CCAGTATGAGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
* *
8325382 TATCTTTGATCTACTTCACGCCAGTACATAAAGATAAGATCTGTTTTCTTCGATCTGCTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
8325447 CCAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
* *
8325471 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATTTGCTTCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
**
8325536 CCAGTACAGGAAGGCAAGATCT-G
66 CCAGTATGGGAAGGCAAGATCTGG
* * *
8325559 TATATTCGATCCACTTC
1 TATCTTTGATCTACTTC
8325576 GCTACCAATA
Statistics
Matches: 342, Mismatches: 29, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
88 92 0.27
89 250 0.73
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (89 bp):
TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
CCAGTATGGGAAGGCAAGATCTGG
Found at i:8333693 original size:20 final size:20
Alignment explanation
Indices: 8333668--8333707 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8333658 TAAAGGTCTT
*
8333668 TAATGCATATAATGCGATGC
1 TAATGCATATAATACGATGC
*
8333688 TAATGCATATGATACGATGC
1 TAATGCATATAATACGATGC
8333708 ATGAGGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TAATGCATATAATACGATGC
Found at i:8337435 original size:15 final size:15
Alignment explanation
Indices: 8337415--8337444 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8337405 ATAATATAAA
8337415 AAAGTATGTAAGTAT
1 AAAGTATGTAAGTAT
*
8337430 AAAGTATGTACGTAT
1 AAAGTATGTAAGTAT
8337445 TTGAAAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.33
Consensus pattern (15 bp):
AAAGTATGTAAGTAT
Found at i:8338789 original size:30 final size:30
Alignment explanation
Indices: 8338755--8338814 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
8338745 TATTTTACTA
*
8338755 TTAATTTTGTTATTATTTTAAAGGCTTTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
8338785 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
8338815 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:8344582 original size:12 final size:12
Alignment explanation
Indices: 8344550--8344583 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
8344540 ACGATCGTGT
*
8344550 TCCA-ACCCGTG
1 TCCATACCCATG
8344561 TCCATACCCATG
1 TCCATACCCATG
8344573 TCCATACCCAT
1 TCCATACCCAT
8344584 TGAACTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.24, C:0.44, G:0.09, T:0.24
Consensus pattern (12 bp):
TCCATACCCATG
Found at i:8345564 original size:21 final size:21
Alignment explanation
Indices: 8345531--8345648 Score: 76
Period size: 21 Copynumber: 5.6 Consensus size: 21
8345521 TACAGAAGCA
* *
8345531 CATAAGTGCTAAACGGAAACC
1 CATAAGGGTTAAACGGAAACC
* *
8345552 CGTAAGGGTTAAACGGAAACT
1 CATAAGGGTTAAACGGAAACC
* * * *
8345573 CATTAGAGCTGAACGGAAACC
1 CATAAGGGTTAAACGGAAACC
* * * *
8345594 TATAAGGGTTAAACTGAAGCT
1 CATAAGGGTTAAACGGAAACC
* * * *
8345615 CAAAAGAGCTAAACTGAAACC
1 CATAAGGGTTAAACGGAAACC
8345636 C-TGAAGGGTTAAA
1 CAT-AAGGGTTAAA
8345649 TTGAAACTCA
Statistics
Matches: 69, Mismatches: 27, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (21 bp):
CATAAGGGTTAAACGGAAACC
Found at i:8345601 original size:42 final size:41
Alignment explanation
Indices: 8345531--8345660 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 41
8345521 TACAGAAGCA
* * *
8345531 CATAAGTGCTAAACGGAAACCCGTAAGGGTTAAACGGAAACT
1 CATAAGAGCTAAACGGAAA-CCTTAAGGGTTAAACTGAAACT
* * *
8345573 CATTAGAGCTGAACGGAAACCTATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACCT-TAAGGGTTAAACTGAAACT
* * * *
8345615 CAAAAGAGCTAAACTGAAACCCTGAAGGGTTAAATTGAAACT
1 CATAAGAGCTAAACGGAAA-CCTTAAGGGTTAAACTGAAACT
8345657 CATA
1 CATA
8345661 TGAGTTAACT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.03
42 67 0.93
43 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (41 bp):
CATAAGAGCTAAACGGAAACCTTAAGGGTTAAACTGAAACT
Found at i:8353029 original size:53 final size:53
Alignment explanation
Indices: 8352971--8353076 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
8352961 GTCGTGTCGA
8352971 GCAGGGCCTGGGCCAAAAACATCTTACTCGAGGCCCAACCTGTTTAGGTAACG
1 GCAGGGCCTGGGCCAAAAACATCTTACTCGAGGCCCAACCTGTTTAGGTAACG
*
8353024 GCAGGGCCTGGGCCAAAAACATCTTACTCGAGGCCCGACCTGTTTAGGTAACG
1 GCAGGGCCTGGGCCAAAAACATCTTACTCGAGGCCCAACCTGTTTAGGTAACG
8353077 AGCCTTATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (53 bp):
GCAGGGCCTGGGCCAAAAACATCTTACTCGAGGCCCAACCTGTTTAGGTAACG
Found at i:8356886 original size:18 final size:18
Alignment explanation
Indices: 8356844--8356888 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
8356834 TTCACTAATT
*
8356844 AATTTAAAT-ATATTTTA
1 AATTTAAATAATATTGTA
*
8356861 AA-AT-AATAATATTGTA
1 AATTTAAATAATATTGTA
8356877 AATTTAAATAAT
1 AATTTAAATAAT
8356889 TTGATTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 3 0.14
18 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATTTAAATAATATTGTA
Found at i:8374534 original size:53 final size:53
Alignment explanation
Indices: 8374454--8374556 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
8374444 TCAACATAGT
* * * *
8374454 ATTGTGAAAGTAGTGCATGAGAATACATGGAAGCCTATTAAATTTTCCAAGTA
1 ATTGTGAAAGTAGTGAATGAGAATACATGAAAGCATATTAAATTTGCCAAGTA
8374507 ATTGTGAAAGTAGTGAATGAGAATACATGAAAGCATATTAAATTTGCCAA
1 ATTGTGAAAGTAGTGAATGAGAATACATGAAAGCATATTAAATTTGCCAA
8374557 TGACGGTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (53 bp):
ATTGTGAAAGTAGTGAATGAGAATACATGAAAGCATATTAAATTTGCCAAGTA
Found at i:8376599 original size:16 final size:15
Alignment explanation
Indices: 8376569--8376609 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
8376559 TTATTTATTA
8376569 AATTAA-TTTAAATT
1 AATTAATTTTAAATT
8376583 AATTAATTTTCAAATT
1 AATTAATTTT-AAATT
*
8376599 AAATAATTTTA
1 AATTAATTTTA
8376610 TAAACCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 4 0.17
16 14 0.58
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTAATTTTAAATT
Found at i:8380282 original size:32 final size:31
Alignment explanation
Indices: 8380228--8380294 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
8380218 CCGAAAACTG
* * *
8380228 TAATTAGATTAAATAATTAAATAGTTAGGAAT
1 TAATTAAATAAAATAATTAAATAATTA-GAAT
8380260 TAATTAAATAAAAT-ATTAAAATAATTAGAAT
1 TAATTAAATAAAATAATT-AAATAATTAGAAT
8380291 TAAT
1 TAAT
8380295 AATTTTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (31 bp):
TAATTAAATAAAATAATTAAATAATTAGAAT
Found at i:8381145 original size:10 final size:10
Alignment explanation
Indices: 8381130--8381160 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
8381120 AGCGAGGTAA
8381130 AGGTTTTGTT
1 AGGTTTTGTT
8381140 AGGTTTTGTT
1 AGGTTTTGTT
8381150 AGGTTTT-TT
1 AGGTTTTGTT
8381159 AG
1 AG
8381161 TCGAGTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (10 bp):
AGGTTTTGTT
Found at i:8384879 original size:36 final size:36
Alignment explanation
Indices: 8384839--8384920 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
8384829 TTGTGAACCA
* *
8384839 TGTTAATTTGGCGAAT-TATATTATTATGGCAAACTG
1 TGTTAATTTGGCG-ATCTATATTAATATGGCAAACGG
* *
8384875 TGTTAATTTGGTGATCTATATTAATATGGCGAACGG
1 TGTTAATTTGGCGATCTATATTAATATGGCAAACGG
*
8384911 TATTAATTTG
1 TGTTAATTTG
8384921 TCAAACTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 2 0.05
36 38 0.95
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (36 bp):
TGTTAATTTGGCGATCTATATTAATATGGCAAACGG
Found at i:8385615 original size:17 final size:16
Alignment explanation
Indices: 8385595--8385651 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
8385585 GAATGCATTA
8385595 TTATATTGAATGAACTG
1 TTAT-TTGAATGAACTG
* *
8385612 TTATTATGCATGAATTG
1 TTATT-TGAATGAACTG
8385629 TTACTTT-ATATGAACTG
1 TTA-TTTGA-ATGAACTG
8385646 TTATTT
1 TTATTT
8385652 TATACAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (16 bp):
TTATTTGAATGAACTG
Found at i:8385653 original size:17 final size:17
Alignment explanation
Indices: 8385604--8385655 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
8385594 ATTATATTGA
* **
8385604 ATGAACTGTTATTATGC
1 ATGAACTGTTATTTTAT
* *
8385621 ATGAATTGTTACTTTAT
1 ATGAACTGTTATTTTAT
8385638 ATGAACTGTTATTTTAT
1 ATGAACTGTTATTTTAT
8385655 A
1 A
8385656 CAAACTGCCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (17 bp):
ATGAACTGTTATTTTAT
Found at i:8388861 original size:19 final size:20
Alignment explanation
Indices: 8388837--8388876 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
8388827 ATTGCTGAAA
8388837 TTATGAGATTTTTG-AAGTT
1 TTATGAGATTTTTGTAAGTT
*
8388856 TTATGATATTTTTGTAAGTT
1 TTATGAGATTTTTGTAAGTT
8388876 T
1 T
8388877 GATAGCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.57
Consensus pattern (20 bp):
TTATGAGATTTTTGTAAGTT
Found at i:8391501 original size:6 final size:6
Alignment explanation
Indices: 8391492--8391521 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
8391482 TTATGTGAGT
8391492 GTGATA GTGATA GTGATA GTGATA GTGATA
1 GTGATA GTGATA GTGATA GTGATA GTGATA
8391522 TGTATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GTGATA
Found at i:8402531 original size:37 final size:37
Alignment explanation
Indices: 8402490--8402576 Score: 156
Period size: 37 Copynumber: 2.4 Consensus size: 37
8402480 ATGCCAAGCA
* *
8402490 CTCATAAGAGCTAATCCAACCGATAACACGCCAAATG
1 CTCATAAGAGCTAATCCAAACGATAACAAGCCAAATG
8402527 CTCATAAGAGCTAATCCAAACGATAACAAGCCAAATG
1 CTCATAAGAGCTAATCCAAACGATAACAAGCCAAATG
8402564 CTCATAAGAGCTA
1 CTCATAAGAGCTA
8402577 TACATCCACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (37 bp):
CTCATAAGAGCTAATCCAAACGATAACAAGCCAAATG
Found at i:8403964 original size:9 final size:9
Alignment explanation
Indices: 8403932--8403964 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
8403922 TCAAGTAAGT
8403932 TTCATTTTC
1 TTCATTTTC
8403941 TTC-TTTTC
1 TTCATTTTC
8403949 ATTCATTTTC
1 -TTCATTTTC
8403959 TTCATT
1 TTCATT
8403965 GCTCCAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 12 0.55
10 5 0.23
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (9 bp):
TTCATTTTC
Found at i:8405871 original size:27 final size:27
Alignment explanation
Indices: 8405841--8405905 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
8405831 TCCATCGGGT
* * **
8405841 TAGTAAACACGGGTTAGTTCATCATGA
1 TAGTAAACACGGGGTAGTCCATCAAAA
*
8405868 TAGTAAACAAGGGGTAGTCCATCAAAA
1 TAGTAAACACGGGGTAGTCCATCAAAA
*
8405895 CAGTAAACACG
1 TAGTAAACACG
8405906 TTAATTATGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTAAACACGGGGTAGTCCATCAAAA
Found at i:8406876 original size:17 final size:17
Alignment explanation
Indices: 8406850--8406883 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8406840 TCTTTTTTTT
*
8406850 TAGGCCTTATGAATAGA
1 TAGGCATTATGAATAGA
*
8406867 TAGGCATTATGAGTAGA
1 TAGGCATTATGAATAGA
8406884 ATAATTGTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (17 bp):
TAGGCATTATGAATAGA
Found at i:8411068 original size:96 final size:96
Alignment explanation
Indices: 8410964--8411286 Score: 442
Period size: 95 Copynumber: 3.4 Consensus size: 96
8410954 AACAACTAGT
* * * *
8410964 TTTATTTGATTTTTTTCTT-AAAACCCTAAATACTAAACCCCAATCTAATTTTTTTAAAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAAAACTAAACCCTAATCTAATTTTTTTAAAATTTAT
8411028 AATTAATTTACTCAAGTAACCCTAGACCCTAA
66 AATTAATTTACTCAAGTAACCCTA-ACCCTAA
* *
8411060 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCT-ATTTTTTT-AAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAAAACTAAACCCTAATCTAATTTTTTTAAAATTTAT
8411123 AATTAATTTACTCAAGTAACCCTAAACCCTAA
66 AATTAATTTACTCAAGTAACCCT-AACCCTAA
* * **
8411155 TTTATTTAATTTTTTCCTTAAAAACCATAAAAACAAAACTATAATCTAA--TTTTTAAAATTTAT
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAAAACTAAACCCTAATCTAATTTTTTTAAAATTTAT
* * * *
8411218 AATTAATTTAATTAAGAAACCCTCAACCCTTA
66 AATTAATTTACTCAAGTAACCCT-AACCCTAA
*
8411250 TTTATTTAATTTTTTCCTT-AAAACCCTAAAATCTAAA
1 TTTATTTAATTTTTTCCTTAAAAACCCTAAAAACTAAA
8411287 AACTCAAAAA
Statistics
Matches: 206, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
94 20 0.10
95 133 0.65
96 28 0.14
97 25 0.12
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (96 bp):
TTTATTTAATTTTTTCCTTAAAAACCCTAAAAACTAAACCCTAATCTAATTTTTTTAAAATTTAT
AATTAATTTACTCAAGTAACCCTAACCCTAA
Found at i:8411432 original size:40 final size:40
Alignment explanation
Indices: 8411377--8411496 Score: 143
Period size: 40 Copynumber: 3.0 Consensus size: 40
8411367 AAGCACTTTG
* * * *
8411377 TCCACGTGGACACAAAGTGCTCCCTCAAGGAAGCGTTTTCTA
1 TCCACGTGG--ACAAAGCGCTTCCTTAAGGAAGCATTTTCTA
* * *
8411419 TCCACGTGGACAAAGCGCTTCCTTGAGGAAGCATTTTTTG
1 TCCACGTGGACAAAGCGCTTCCTTAAGGAAGCATTTTCTA
8411459 T-CATCGTGGACAAAGCGCTTCCTTAAGGAAGCATTTTC
1 TCCA-CGTGGACAAAGCGCTTCCTTAAGGAAGCATTTTC
8411497 CTGCTTTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.03
40 57 0.84
42 9 0.13
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (40 bp):
TCCACGTGGACAAAGCGCTTCCTTAAGGAAGCATTTTCTA
Found at i:8419774 original size:22 final size:23
Alignment explanation
Indices: 8419748--8419792 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
8419738 AGGTATCCAC
*
8419748 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCCAAGATTACA
*
8419770 AAATCATATCTTCCAAGATTACA
1 AAATCAAATCTTCCAAGATTACA
8419793 TATCATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATCAAATCTTCCAAGATTACA
Found at i:8419791 original size:23 final size:22
Alignment explanation
Indices: 8419746--8419802 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
8419736 AAAGGTATCC
* *
8419746 ACAAATCAAATC-TCTAAGATT
1 ACAAATCATATCTTCCAAGATT
8419767 ACAAAATCATATCTTCCAAGATT
1 AC-AAATCATATCTTCCAAGATT
*
8419790 ACATATCATATCT
1 ACAAATCATATCT
8419803 ACGGTTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.06
22 19 0.61
23 10 0.32
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (22 bp):
ACAAATCATATCTTCCAAGATT
Found at i:8420810 original size:17 final size:17
Alignment explanation
Indices: 8420796--8420839 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
8420786 ATAATCTTCA
8420796 AGGATATGCAATCTTAG
1 AGGATATGCAATCTTAG
*
8420813 ATATGATATGCAATCTTAG
1 --AGGATATGCAATCTTAG
8420832 AGGATATG
1 AGGATATG
8420840 ATTTTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
19 16 0.70
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (17 bp):
AGGATATGCAATCTTAG
Found at i:8424016 original size:23 final size:24
Alignment explanation
Indices: 8423965--8424010 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
8423955 CAATCATTGT
*
8423965 ATTGCACTGAAGTGCCACATTTCG
1 ATTGCACCGAAGTGCCACATTTCG
8423989 ATTGCACCGAAGTGCCAC-TTTC
1 ATTGCACCGAAGTGCCACATTTC
8424011 ATTTGCGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (24 bp):
ATTGCACCGAAGTGCCACATTTCG
Found at i:8427746 original size:12 final size:12
Alignment explanation
Indices: 8427719--8427760 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
8427709 ATTTATTTAG
8427719 AAAATTAATAATA
1 AAAATTAA-AATA
*
8427732 AAAATTAAAA-G
1 AAAATTAAAATA
*
8427743 AAAATGAAAATA
1 AAAATTAAAATA
8427755 AAAATT
1 AAAATT
8427761 TAATGGTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.38
12 7 0.29
13 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (12 bp):
AAAATTAAAATA
Found at i:8428680 original size:12 final size:12
Alignment explanation
Indices: 8428665--8428691 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8428655 AATAATAATC
8428665 AAAATTTTGTTT
1 AAAATTTTGTTT
8428677 AAAATTTTGTTT
1 AAAATTTTGTTT
8428689 AAA
1 AAA
8428692 TGAGTGCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
AAAATTTTGTTT
Found at i:8433645 original size:11 final size:10
Alignment explanation
Indices: 8433616--8433649 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
8433606 TTAAAATCTT
8433616 AAATTAAAAC
1 AAATTAAAAC
*
8433626 ATATTAAAAC
1 AAATTAAAAC
8433636 AAATTTAAAAC
1 AAA-TTAAAAC
8433647 AAA
1 AAA
8433650 AACGTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATTAAAAC
Found at i:8434300 original size:31 final size:31
Alignment explanation
Indices: 8434230--8434341 Score: 145
Period size: 31 Copynumber: 3.5 Consensus size: 31
8434220 TAGTATGATA
* *
8434230 ATTAAATTAAATT-AATTAGTATATAATGTGAT
1 ATTAAATTAAATTAAAATATTATATAATGT--T
8434262 AAAATTAAATTAAATTAAAATATTATATAATGTT
1 ---ATTAAATTAAATTAAAATATTATATAATGTT
8434296 ATTAAATTAAATTAAAATATTATATAATGTT
1 ATTAAATTAAATTAAAATATTATATAATGTT
*
8434327 ATTAAATTAAGTTAA
1 ATTAAATTAAATTAA
8434342 TAATGGGTCT
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
31 45 0.62
34 1 0.01
35 13 0.18
36 14 0.19
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
ATTAAATTAAATTAAAATATTATATAATGTT
Found at i:8434533 original size:3 final size:3
Alignment explanation
Indices: 8434525--8434557 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
8434515 ATGTTCAAAG
*
8434525 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8434558 ATGGCAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:8448023 original size:24 final size:24
Alignment explanation
Indices: 8447972--8448023 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
8447962 TTCGTAGGTC
*
8447972 AAATAAATTACACTAATAAATGCA
1 AAATAAATTACACTAATAAATACA
* * * *
8447996 AAATATATTATACTACTAAATACT
1 AAATAAATTACACTAATAAATACA
8448020 AAAT
1 AAAT
8448024 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAAATTACACTAATAAATACA
Found at i:8451920 original size:9 final size:9
Alignment explanation
Indices: 8451906--8451946 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
8451896 TCCTATGAGT
8451906 TTAAAAAAA
1 TTAAAAAAA
8451915 TT-AAAAAA
1 TTAAAAAAA
8451923 TTAAAAAAA
1 TTAAAAAAA
*
8451932 TCAAAAAAA
1 TTAAAAAAA
*
8451941 TGAAAA
1 TTAAAA
8451947 TGAAAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:8451928 original size:17 final size:17
Alignment explanation
Indices: 8451906--8451939 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8451896 TCCTATGAGT
*
8451906 TTAAAAAAATTAAAAAA
1 TTAAAAAAATCAAAAAA
8451923 TTAAAAAAATCAAAAAA
1 TTAAAAAAATCAAAAAA
8451940 ATGAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TTAAAAAAATCAAAAAA
Found at i:8451937 original size:6 final size:6
Alignment explanation
Indices: 8451937--8452015 Score: 85
Period size: 6 Copynumber: 13.7 Consensus size: 6
8451927 AAAAATCAAA
*
8451937 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG ---ATGG AAAAAG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT-G AAAATG
* * *
8451983 -AAATG AAAATG AAAAAG AAAAAG AAAAGG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
8452016 GGAGAGGCCA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 4 0.06
6 56 0.88
7 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (6 bp):
AAAATG
Found at i:8451946 original size:17 final size:17
Alignment explanation
Indices: 8451907--8451946 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
8451897 CCTATGAGTT
* *
8451907 TAAAAAAATTAAAAAAT
1 TAAAAAAATCAAAAAAA
8451924 TAAAAAAATCAAAAAAA
1 TAAAAAAATCAAAAAAA
8451941 TGAAAA
1 T-AAAA
8451947 TGAAAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
TAAAAAAATCAAAAAAA
Found at i:8456310 original size:32 final size:31
Alignment explanation
Indices: 8456273--8456334 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
8456263 TCTGTAATTC
*
8456273 TATAAC-TTTTAATATATTTTGTATATTTTATT
1 TATAACATTTTAAT-TATTTTATAT-TTTTATT
8456305 TATAACATTTTAATTATTTTATATTTTTAT
1 TATAACATTTTAATTATTTTATATTTTTAT
8456335 GCCTACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 6 0.21
32 15 0.54
33 7 0.25
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (31 bp):
TATAACATTTTAATTATTTTATATTTTTATT
Found at i:8456603 original size:39 final size:39
Alignment explanation
Indices: 8456528--8456603 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
8456518 ATGAAAAATG
* * * * *
8456528 TTAGATATTTTGGTATTTGGTGACAAATTTGGGTATCCT
1 TTAGAAATTTTAGTATTTGATGAAAAATTTGAGTATCCT
* *
8456567 TTAGAAATTTTAGTATTTGATTAAAAATTTTAGTATC
1 TTAGAAATTTTAGTATTTGATGAAAAATTTGAGTATC
8456604 ATCTATTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (39 bp):
TTAGAAATTTTAGTATTTGATGAAAAATTTGAGTATCCT
Found at i:8456715 original size:19 final size:19
Alignment explanation
Indices: 8456688--8456811 Score: 76
Period size: 19 Copynumber: 6.4 Consensus size: 19
8456678 AATTTTGGTG
*
8456688 TTTTGGTATTCGTTAGAAA
1 TTTTAGTATTCGTTAGAAA
*
8456707 TTTTAGTA-TCTATTAGAAA
1 TTTTAGTATTC-GTTAGAAA
* *
8456726 TTTTAGTATGCG-TACTAAA
1 TTTTAGTATTCGTTA-GAAA
* * *
8456745 TTTTGGTATCCGTTAAAAA
1 TTTTAGTATTCGTTAGAAA
* *
8456764 CTTTT-GATATTTGGTTACAAA
1 -TTTTAG-TA-TTCGTTAGAAA
*
8456785 TTTTTGTA-TCTGTTAGAAA
1 TTTTAGTATTC-GTTAGAAA
8456804 TTTTAGTA
1 TTTTAGTA
8456812 CAATCCATTA
Statistics
Matches: 82, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
18 5 0.06
19 53 0.65
20 15 0.18
21 9 0.11
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (19 bp):
TTTTAGTATTCGTTAGAAA
Found at i:8464765 original size:31 final size:31
Alignment explanation
Indices: 8464730--8464793 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
8464720 CTCATCTCAT
8464730 AAATTTAACATTG-AATTTTACTAATTTTATA
1 AAATTTAACA-TGCAATTTTACTAATTTTATA
*
8464761 AAATTTAACATGCAATTTTACTACTTTTATA
1 AAATTTAACATGCAATTTTACTAATTTTATA
8464792 AA
1 AA
8464794 TAAGTCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (31 bp):
AAATTTAACATGCAATTTTACTAATTTTATA
Found at i:8472293 original size:23 final size:23
Alignment explanation
Indices: 8472259--8472316 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
8472249 TTGGTGGGAG
*
8472259 CATTTTGACACTTTGATGCATAT
1 CATTTTGGCACTTTGATGCATAT
*
8472282 CATTTTGGCACTTTGGTGCATAT
1 CATTTTGGCACTTTGATGCATAT
8472305 CATTTTGGCACT
1 CATTTTGGCACT
8472317 ACGGTGCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (23 bp):
CATTTTGGCACTTTGATGCATAT
Found at i:8472322 original size:23 final size:23
Alignment explanation
Indices: 8472275--8472327 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
8472265 GACACTTTGA
**
8472275 TGCATATCATTTTGGCACTTTGG
1 TGCATATCATTTTGGCACTACGG
8472298 TGCATATCATTTTGGCACTACGG
1 TGCATATCATTTTGGCACTACGG
8472321 TGCATAT
1 TGCATAT
8472328 TATACTATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (23 bp):
TGCATATCATTTTGGCACTACGG
Found at i:8493871 original size:30 final size:29
Alignment explanation
Indices: 8493814--8493895 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
8493804 ACATCATGAG
*
8493814 TAATCCAATTATTGTCTCTTTTT-ATTTTTA
1 TAATCCAATTATTAT-T-TTTTTAATTTTTA
* * *
8493844 TCATCTAATTATTAATTTTTTTAATTTTTT
1 TAATCCAATTATT-ATTTTTTTAATTTTTA
*
8493874 TAATCCAATTATTGTTTTTTTA
1 TAATCCAATTATTATTTTTTTA
8493896 CCTAACTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 13 0.30
30 29 0.67
31 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (29 bp):
TAATCCAATTATTATTTTTTTAATTTTTA
Found at i:8494978 original size:60 final size:61
Alignment explanation
Indices: 8494902--8495016 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 61
8494892 AAAATTCAAT
*
8494902 TAGTTGAGTAACCAAATAAAAAAAATTGATAATTAGGTGA-TAA-AAAAAGAAAAGGGGCAA
1 TAGTTGAATAACCAAATAAAAAAAATTGATAATTAGGTGACTAATAAAAA-AAAAGGGGCAA
* * * * *
8494962 TAGTTGAATGACCAAATTAAAAATATTGATAGTTGGGTGACTAATAAAAAAAAAG
1 TAGTTGAATAACCAAATAAAAAAAATTGATAATTAGGTGACTAATAAAAAAAAAG
8495017 ATAATAGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 34 0.72
61 8 0.17
62 5 0.11
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.23
Consensus pattern (61 bp):
TAGTTGAATAACCAAATAAAAAAAATTGATAATTAGGTGACTAATAAAAAAAAAGGGGCAA
Found at i:8495738 original size:19 final size:20
Alignment explanation
Indices: 8495716--8495767 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
8495706 TTATTTTTTT
8495716 AAAATT-TTAAAAACAATTAA
1 AAAATTATTAAAAA-AATTAA
**
8495736 AAAATTATTTTAAAAATT-A
1 AAAATTATTAAAAAAATTAA
8495755 AAAATTATTAAAA
1 AAAATTATTAAAA
8495768 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.44
20 10 0.37
21 5 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTATTAAAAAAATTAA
Found at i:8495758 original size:30 final size:28
Alignment explanation
Indices: 8495712--8495787 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
8495702 TTAATTATTT
*
8495712 TTTTAAAATTTTAAAAACAATTAAAAAATTA
1 TTTTAAAA-ATTAAAAACAATT--AAAATTA
**
8495743 TTTTAAAAATTAAAAATTATTAAAATTA
1 TTTTAAAAATTAAAAACAATTAAAATTA
*
8495771 TTTTAAAAGTATAAAAA
1 TTTTAAAAAT-TAAAAA
8495788 GTACAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 16 0.40
29 6 0.15
30 10 0.25
31 8 0.20
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTTAAAAATTAAAAACAATTAAAATTA
Found at i:8495795 original size:28 final size:28
Alignment explanation
Indices: 8495736--8495795 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
8495726 AAACAATTAA
* *
8495736 AAAATTATTTTAAAAATTAAAAATTATT
1 AAAATTATTTTAAAAATTAAAAAGTATC
*
8495764 AAAATTATTTTAAAAGTATAAAAAGTA-C
1 AAAATTATTTTAAAAAT-TAAAAAGTATC
8495792 AAAA
1 AAAA
8495796 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTATTTTAAAAATTAAAAAGTATC
Found at i:8495796 original size:29 final size:28
Alignment explanation
Indices: 8495735--8495803 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
8495725 AAAACAATTA
* *
8495735 AAAAATTATTTTAAAAATTAAAAATTAT
1 AAAAATTATTTTAAAAATTAAAAAGTAC
* *
8495763 TAAAATTATTTTAAAAGTATAAAAAGTAC
1 AAAAATTATTTTAAAAAT-TAAAAAGTAC
*
8495792 AAAAAATATTTT
1 AAAAATTATTTT
8495804 TATTTTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 16 0.47
29 18 0.53
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAAATTATTTTAAAAATTAAAAAGTAC
Found at i:8497170 original size:11 final size:11
Alignment explanation
Indices: 8497154--8497179 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8497144 AGTTTATGTA
8497154 TTTTCTTATTG
1 TTTTCTTATTG
8497165 TTTTCTTATTG
1 TTTTCTTATTG
8497176 TTTT
1 TTTT
8497180 GGTTGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTCTTATTG
Found at i:8498207 original size:37 final size:35
Alignment explanation
Indices: 8498152--8498228 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 35
8498142 TATTGTTACT
8498152 ATTGAATGCATGACAAGCATGCCACCAATACTGATAA
1 ATTGAATGCATGACAAGCATGCCACCAATACT-A-AA
** * *
8498189 ATTGAATGCATGTTAAGCATGCCATCATTACTAAA
1 ATTGAATGCATGACAAGCATGCCACCAATACTAAA
8498224 ATTGA
1 ATTGA
8498229 TATTGATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 7 0.19
36 1 0.03
37 28 0.78
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (35 bp):
ATTGAATGCATGACAAGCATGCCACCAATACTAAA
Found at i:8499848 original size:20 final size:20
Alignment explanation
Indices: 8499823--8499868 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
8499813 TTAAGTTTTC
*
8499823 TTAAAAGAAATCAATACTTG
1 TTAAAAGAAATCAATACTTA
**
8499843 TTAAAAAGGTATCAATACTTA
1 TT-AAAAGAAATCAATACTTA
8499864 TTAAA
1 TTAAA
8499869 GTATCGATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TTAAAAGAAATCAATACTTA
Found at i:8502824 original size:46 final size:46
Alignment explanation
Indices: 8502757--8502887 Score: 156
Period size: 46 Copynumber: 2.8 Consensus size: 46
8502747 ATTTTTACCT
**
8502757 AGGTTCCTAGCTCCTGCATATGTTGTGGACTAGAGAATACAG-ATTC
1 AGGTTCCTAGCTCCTGCATATGTTGCAGACTAGAGAATA-AGAATTC
* * * *
8502803 AGGTTCCTAGCTCCTACATATGTTGCAGACTGGAGAATAGGAATTT
1 AGGTTCCTAGCTCCTGCATATGTTGCAGACTAGAGAATAAGAATTC
* * * *
8502849 AGGTTCCCAGCTCATGCATATGTTGCAAACTGGAGAATA
1 AGGTTCCTAGCTCCTGCATATGTTGCAGACTAGAGAATA
8502888 CGAAATATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 73 0.99
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (46 bp):
AGGTTCCTAGCTCCTGCATATGTTGCAGACTAGAGAATAAGAATTC
Found at i:8510475 original size:20 final size:20
Alignment explanation
Indices: 8510437--8510489 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
8510427 ATGCAATATA
* *
8510437 TTCTTC-TCTTCTTCTTCCTT
1 TTCTTCTTCTTTTTC-TCCTC
*
8510457 TTCTTTTTCTTTTTCTCCTC
1 TTCTTCTTCTTTTTCTCCTC
8510477 TTCTTCTTCTTTT
1 TTCTTCTTCTTTT
8510490 ACTATTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTTCTTCTTTTTCTCCTC
Found at i:8510661 original size:20 final size:20
Alignment explanation
Indices: 8510636--8510673 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8510626 TTGTTATTTT
*
8510636 TTGAAAGTTAAGTGATTGAG
1 TTGAAAATTAAGTGATTGAG
*
8510656 TTGAAAATTGAGTGATTG
1 TTGAAAATTAAGTGATTG
8510674 TTTTGTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (20 bp):
TTGAAAATTAAGTGATTGAG
Found at i:8511350 original size:23 final size:23
Alignment explanation
Indices: 8511324--8511377 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
8511314 ATTCATAAAA
8511324 AAAAATTCA-AAATAAAAAATTTT
1 AAAAATT-ATAAATAAAAAATTTT
* * *
8511347 AAAAAATATACATAAAAACTTTT
1 AAAAATTATAAATAAAAAATTTT
8511370 AGAAAATT
1 A-AAAATT
8511378 TATCCATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 19 0.76
24 5 0.20
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAATTATAAATAAAAAATTTT
Found at i:8511767 original size:20 final size:21
Alignment explanation
Indices: 8511730--8511769 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
8511720 TCTCCCCTGC
8511730 ATTTACACTAAAAGAAAATAA
1 ATTTACACTAAAAGAAAATAA
* *
8511751 ATTTAC-CTAATATAAAATA
1 ATTTACACTAAAAGAAAATA
8511770 GTTGAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (21 bp):
ATTTACACTAAAAGAAAATAA
Found at i:8515897 original size:11 final size:11
Alignment explanation
Indices: 8515877--8515973 Score: 50
Period size: 11 Copynumber: 9.4 Consensus size: 11
8515867 TAAAAATTAA
8515877 AAAAAGTATTTT
1 AAAAA-TATTTT
8515889 AAAAATATTTT
1 AAAAATATTTT
8515900 --AAA-A--TT
1 AAAAATATTTT
* * *
8515906 AAAAAAAATTA
1 AAAAATATTTT
8515917 AAAAAGTATTTT
1 AAAAA-TATTTT
*
8515929 AAAAAAATTTT
1 AAAAATATTTT
8515940 --AAA-ATTTT
1 AAAAATATTTT
*
8515948 AAAAAT-TTAAT
1 AAAAATATT-TT
*
8515959 AAAAGTATTTT
1 AAAAATATTTT
8515970 AAAA
1 AAAA
8515974 TTAAAAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
6 2 0.03
8 9 0.14
9 7 0.11
10 5 0.08
11 28 0.42
12 15 0.23
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:8515920 original size:41 final size:41
Alignment explanation
Indices: 8515844--8515973 Score: 172
Period size: 40 Copynumber: 3.1 Consensus size: 41
8515834 ATAAATACCA
8515844 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTT
8515889 AAAAATATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
* ** * *
8515929 AAAAAAATTTTAAAATTTTAAAAATTTAATAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
8515970 AAAA
1 AAAA
8515974 TTAAAAAAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
40 36 0.46
41 23 0.29
42 3 0.04
43 6 0.08
44 6 0.08
45 5 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (41 bp):
AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
Found at i:8515982 original size:30 final size:27
Alignment explanation
Indices: 8515910--8515983 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 27
8515900 AAAATTAAAA
8515910 AAAATTAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAA--A-TTTAAAAAAATTTT
**
8515940 AAAATTTTAAAAATTTAATAAAAGTATTTT
1 AAAATTAAAAAAATTTAA-AAAA--ATTTT
8515970 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
8515984 AAAAAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 5 0.14
28 5 0.14
30 27 0.73
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AAAATTAAAAAAATTTAAAAAAATTTT
Found at i:8529652 original size:22 final size:22
Alignment explanation
Indices: 8529627--8529669 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
8529617 TTATTTGGCG
*
8529627 TTTGAGATAGACGTTGTTATAA
1 TTTGAGATAGACATTGTTATAA
8529649 TTTGAGATAGACATTGTTATA
1 TTTGAGATAGACATTGTTATA
8529670 GTTTTAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (22 bp):
TTTGAGATAGACATTGTTATAA
Found at i:8532321 original size:28 final size:28
Alignment explanation
Indices: 8532269--8532327 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
8532259 AAAAACTTTG
* * * *
8532269 GAATTGGGAATTTAGATTAAAAAATTGA
1 GAATTGAGAATTGAGAATAAAAAATCGA
*
8532297 GAATTGAGAATTGAGAATAACAAATCGA
1 GAATTGAGAATTGAGAATAAAAAATCGA
8532325 GAA
1 GAA
8532328 CAATAAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.25
Consensus pattern (28 bp):
GAATTGAGAATTGAGAATAAAAAATCGA
Found at i:8533717 original size:24 final size:22
Alignment explanation
Indices: 8533665--8533717 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 22
8533655 TTCACAAGTA
* *
8533665 ATTTTAAAATTTGTCATTTTTT
1 ATTTTAAAATTTATCATTTTAT
*
8533687 ATCTTTAAATATTTATTATTTTAAT
1 AT-TTTAAA-ATTTATCATTTT-AT
8533712 ATTTTA
1 ATTTTA
8533718 CTATACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 6 0.24
24 14 0.56
25 3 0.12
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTTAAAATTTATCATTTTAT
Found at i:8534085 original size:13 final size:14
Alignment explanation
Indices: 8534069--8534099 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
8534059 CTCATTTTAT
8534069 TTTTTTA-AATTAA
1 TTTTTTAGAATTAA
8534082 TTTTTTAGAATTAA
1 TTTTTTAGAATTAA
8534096 TTTT
1 TTTT
8534100 AGTTTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTTTTAGAATTAA
Found at i:8534086 original size:14 final size:15
Alignment explanation
Indices: 8534067--8534099 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
8534057 TACTCATTTT
8534067 ATTTTTTTA-AATTA
1 ATTTTTTTAGAATTA
8534081 A-TTTTTTAGAATTA
1 ATTTTTTTAGAATTA
8534095 ATTTT
1 ATTTT
8534100 AGTTTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 7 0.41
15 3 0.18
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
ATTTTTTTAGAATTA
Found at i:8534424 original size:20 final size:20
Alignment explanation
Indices: 8534401--8534469 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
8534391 TTTGGGGCTC
*
8534401 AAGGTTTAGG-TTCGAGGTTG
1 AAGGTTTAGGCTTAG-GGTTG
* *
8534421 AAGGTTTGGGCTTAGGGTTT
1 AAGGTTTAGGCTTAGGGTTG
* * *
8534441 AAGGTTTAGGGTTTTGGGTTC
1 AAGGTTTA-GGCTTAGGGTTG
8534462 AAGGTTTA
1 AAGGTTTA
8534470 AGATTCAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 20 0.50
21 20 0.50
ACGTcount: A:0.19, C:0.04, G:0.38, T:0.39
Consensus pattern (20 bp):
AAGGTTTAGGCTTAGGGTTG
Found at i:8534522 original size:14 final size:14
Alignment explanation
Indices: 8534436--8534522 Score: 59
Period size: 14 Copynumber: 6.2 Consensus size: 14
8534426 TTGGGCTTAG
* *
8534436 GGTTTAAGGTTTAG
1 GGTTTAAGGTTCAA
**
8534450 GGTTTTGGGTTCAA
1 GGTTTAAGGTTCAA
*
8534464 GGTTTAAGATTCAA
1 GGTTTAAGGTTCAA
* *
8534478 GATTTAAGATTC-A
1 GGTTTAAGGTTCAA
*** *
8534491 GAGTTGGGGGTTCTA
1 G-GTTTAAGGTTCAA
8534506 GGTTTAAGGTTCAA
1 GGTTTAAGGTTCAA
8534520 GGT
1 GGT
8534523 AAAAGAAAAT
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
13 2 0.04
14 50 0.93
15 2 0.04
ACGTcount: A:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (14 bp):
GGTTTAAGGTTCAA
Found at i:8535136 original size:22 final size:21
Alignment explanation
Indices: 8535097--8535138 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8535087 GATTATACAT
*
8535097 TAAAAATCCATAAAAATAATG
1 TAAAAATCAATAAAAATAATG
*
8535118 TAAAAATCAAGTAAGAATAAT
1 TAAAAATCAA-TAAAAATAAT
8535139 CCAAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (21 bp):
TAAAAATCAATAAAAATAATG
Found at i:8540173 original size:33 final size:33
Alignment explanation
Indices: 8540136--8540214 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
8540126 TAGTTCGCCA
* *
8540136 GGACAGTAAACACAAAACAAAGATAGTATGTTG
1 GGACAGTAAACACAAAACAAAGATAATATGTCG
* * *
8540169 GGACATTAAACACAAAACAGAGATAATTTGTCG
1 GGACAGTAAACACAAAACAAAGATAATATGTCG
8540202 GGACAGTAAACAC
1 GGACAGTAAACAC
8540215 GAGGTAAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (33 bp):
GGACAGTAAACACAAAACAAAGATAATATGTCG
Found at i:8551389 original size:18 final size:17
Alignment explanation
Indices: 8551362--8551395 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
8551352 CTTCTGTATC
8551362 AAATATTTAAAATAAAT
1 AAATATTTAAAATAAAT
*
8551379 AAATAATTTAAAGTAAA
1 AAAT-ATTTAAAATAAA
8551396 AACCAAGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATATTTAAAATAAAT
Found at i:8552942 original size:26 final size:26
Alignment explanation
Indices: 8552906--8552960 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
8552896 TGTGTTCAAT
8552906 CTAGATACCATGGGAAAATGTATGAA
1 CTAGATACCATGGGAAAATGTATGAA
8552932 CTAGATACCATGGGAAAATGTATGAA
1 CTAGATACCATGGGAAAATGTATGAA
8552958 CTA
1 CTA
8552961 TACGATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (26 bp):
CTAGATACCATGGGAAAATGTATGAA
Found at i:8556387 original size:7 final size:8
Alignment explanation
Indices: 8556368--8556398 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
8556358 TTTTATGAAT
8556368 TTTTTTAA
1 TTTTTTAA
8556376 TTTTTTAA
1 TTTTTTAA
8556384 TTTTTTAA
1 TTTTTTAA
*
8556392 TTATTTA
1 TTTTTTA
8556399 TTGACGTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTAA
Found at i:8570306 original size:34 final size:34
Alignment explanation
Indices: 8570245--8570311 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
8570235 AAATTTGAGT
*
8570245 GAAATATAGGGATCAAAATTGATATTTAACCATA
1 GAAATATAGGGATCAAAATTGAAATTTAACCATA
* * *
8570279 GAAAT-TAGAGGATTAAATTTGAAATTTAGCCAT
1 GAAATATAG-GGATCAAAATTGAAATTTAACCAT
8570312 TTTATTGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.31
Consensus pattern (34 bp):
GAAATATAGGGATCAAAATTGAAATTTAACCATA
Found at i:8579850 original size:16 final size:17
Alignment explanation
Indices: 8579824--8579858 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
8579814 TAGAATTGGG
*
8579824 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
8579841 TTGA-AAAATTAATTAA
1 TTGAGAAAATTAATTAA
8579857 TT
1 TT
8579859 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:8582428 original size:15 final size:14
Alignment explanation
Indices: 8582408--8582449 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
8582398 CCCAATAATT
8582408 TAATATCTCCAAATA
1 TAATAT-TCCAAATA
* *
8582423 TAATATTTCATATA
1 TAATATTCCAAATA
8582437 T-ATATTCCAAATA
1 TAATATTCCAAATA
8582450 AAATGACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.43
14 7 0.30
15 6 0.26
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATATTCCAAATA
Found at i:8591938 original size:22 final size:23
Alignment explanation
Indices: 8591904--8591946 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8591894 AATTTATCAC
8591904 AATTTATATTAAA-ATAATAATAA
1 AATTTATATTAAATAT-ATAATAA
8591927 AATTTATA-TAAATATATAAT
1 AATTTATATTAAATATATAAT
8591947 GTCTCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTTATATTAAATATATAATAA
Found at i:8592660 original size:14 final size:14
Alignment explanation
Indices: 8592641--8592671 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8592631 ATTATTGTTT
*
8592641 TAATCTAAATTTAC
1 TAATCTAAATTAAC
8592655 TAATCTAAATTAAC
1 TAATCTAAATTAAC
8592669 TAA
1 TAA
8592672 GAACACGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:8596982 original size:31 final size:33
Alignment explanation
Indices: 8596913--8596984 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
8596903 CAAGAAGCAA
*
8596913 ACTAAACTAATGAAATGAAGCAGAATAAAAGAG
1 ACTAAACTAATGAAATGAAGCAAAATAAAAGAG
*
8596946 A--AAACTAATG-AAT-AATG-AAAATAAAATAG
1 ACTAAACTAATGAAATGAA-GCAAAATAAAAGAG
8596975 ACTAAACTAA
1 ACTAAACTAA
8596985 AAGGGACAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 16 0.47
33 1 0.03
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.18
Consensus pattern (33 bp):
ACTAAACTAATGAAATGAAGCAAAATAAAAGAG
Found at i:8597114 original size:25 final size:26
Alignment explanation
Indices: 8597084--8597139 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
8597074 ATCATAAAAA
8597084 AATAACAA-GTAAAAAAAAC-AATAAG
1 AATAACAATG-AAAAAAAACAAATAAG
*
8597109 AATAACAATGAAAAATAACAAATAAG
1 AATAACAATGAAAAAAAACAAATAAG
8597135 AATAA
1 AATAA
8597140 TAAGAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (26 bp):
AATAACAATGAAAAAAAACAAATAAG
Found at i:8597127 original size:13 final size:13
Alignment explanation
Indices: 8597081--8597129 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
8597071 AGAATCATAA
8597081 AAAAATAACAA-G
1 AAAAATAACAATG
*
8597093 TAAAAAAAACAAT-
1 -AAAAATAACAATG
*
8597106 AAGAATAACAATG
1 AAAAATAACAATG
8597119 AAAAATAACAA
1 AAAAATAACAA
8597130 ATAAGAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAATAACAATG
Found at i:8597138 original size:13 final size:13
Alignment explanation
Indices: 8597067--8597139 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
8597057 AACTAACAAT
* *
8597067 AATAAGAATCATA
1 AATAAGAATAACA
8597080 AA-AA-AATAACA
1 AATAAGAATAACA
* * *
8597091 AGTAAAAAAAAC-
1 AATAAGAATAACA
8597103 AATAAGAATAAC-
1 AATAAGAATAACA
*
8597115 AATGAAAAATAACA
1 AAT-AAGAATAACA
8597129 AATAAGAATAA
1 AATAAGAATAA
8597140 TAAGAATAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
11 6 0.13
12 16 0.34
13 22 0.47
14 3 0.06
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (13 bp):
AATAAGAATAACA
Found at i:8597151 original size:38 final size:36
Alignment explanation
Indices: 8597081--8597175 Score: 91
Period size: 38 Copynumber: 2.5 Consensus size: 36
8597071 AGAATCATAA
* * *
8597081 AAAAATAACAAGTAAAAAAAACAATAAGAATAACAATG
1 AAAAATAACAAAT-AAAATAACAAGAAGAATAACAA-G
* * *
8597119 AAAAATAACAAATAAGAATAATAAGAATAATAATAAG
1 AAAAATAACAAATAA-AATAACAAGAAGAATAACAAG
*
8597156 AATAATAACTAAATAAAATA
1 AAAAATAAC-AAATAAAATA
8597176 TAGGGGCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 15 0.31
38 33 0.69
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (36 bp):
AAAAATAACAAATAAAATAACAAGAAGAATAACAAG
Found at i:8597152 original size:12 final size:12
Alignment explanation
Indices: 8597064--8597163 Score: 64
Period size: 12 Copynumber: 8.4 Consensus size: 12
8597054 AACAACTAAC
8597064 AATAATAAGAAT
1 AATAATAAGAAT
* *
8597076 CATAA-AAAAAT
1 AATAATAAGAAT
* * *
8597087 AACAAGTAAAAAA
1 AATAA-TAAGAAT
*
8597100 AACAATAAGAAT
1 AATAATAAGAAT
* *
8597112 AACAATGAAAAAT
1 AATAAT-AAGAAT
*
8597125 AACAAATAAG---
1 AA-TAATAAGAAT
8597135 AATAATAAGAAT
1 AATAATAAGAAT
8597147 AATAATAAGAAT
1 AATAATAAGAAT
8597159 AATAA
1 AATAA
8597164 CTAAATAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
9 6 0.09
10 2 0.03
11 8 0.11
12 32 0.46
13 19 0.27
14 3 0.04
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (12 bp):
AATAATAAGAAT
Found at i:8597163 original size:9 final size:9
Alignment explanation
Indices: 8597064--8597151 Score: 56
Period size: 9 Copynumber: 9.9 Consensus size: 9
8597054 AACAACTAAC
8597064 AATAATAAG
1 AATAATAAG
*
8597073 AATCATAA-
1 AATAATAAG
* *
8597081 AAAAATAAC
1 AATAATAAG
* *
8597090 AAGTAAAAAA
1 AA-TAATAAG
*
8597100 AACAATAAG
1 AATAATAAG
*
8597109 AATAACAATG
1 AATAATAA-G
*
8597119 AAAAATAA-
1 AATAATAAG
*
8597127 CA-AATAAG
1 AATAATAAG
8597135 AATAATAAG
1 AATAATAAG
8597144 AATAATAA
1 AATAATAA
8597152 TAAGAATAAT
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
7 5 0.08
8 8 0.14
9 33 0.56
10 13 0.22
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (9 bp):
AATAATAAG
Found at i:8606070 original size:34 final size:35
Alignment explanation
Indices: 8606012--8606078 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
8606002 CAAACACCAG
8606012 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
8606047 AAAATATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
8606079 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:8608021 original size:20 final size:21
Alignment explanation
Indices: 8607998--8608036 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
8607988 AGGTATAATG
*
8607998 AACTTAAAAAT-TATAAAAAA
1 AACTCAAAAATCTATAAAAAA
*
8608018 AACTCAAAATTCTATAAAA
1 AACTCAAAAATCTATAAAA
8608037 CCCTAAACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (21 bp):
AACTCAAAAATCTATAAAAAA
Found at i:8610586 original size:8 final size:8
Alignment explanation
Indices: 8610574--8610614 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
8610564 GAATCTTCAG
*
8610574 GTGGGTGG
1 GTGGGTGT
8610582 GTGGGTGT
1 GTGGGTGT
*
8610590 GTGTGTGT
1 GTGGGTGT
*
8610598 GTGTGTGT
1 GTGGGTGT
8610606 GTGGGTGT
1 GTGGGTGT
8610614 G
1 G
8610615 GGAGAGGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (8 bp):
GTGGGTGT
Found at i:8613048 original size:16 final size:16
Alignment explanation
Indices: 8613027--8613072 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
8613017 AATTGGGTTG
*
8613027 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
8613043 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
8613059 --AAAATTAATGTAAT
1 AGAAAATTAAT-TAAT
8613073 AAATAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:8618373 original size:17 final size:18
Alignment explanation
Indices: 8618341--8618380 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
8618331 ATGTTCACGG
8618341 AATTTGAATTTAATTTAT
1 AATTTGAATTTAATTTAT
* *
8618359 AATTT-AATTTTATTTCT
1 AATTTGAATTTAATTTAT
8618376 AATTT
1 AATTT
8618381 CTTGAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
AATTTGAATTTAATTTAT
Found at i:8625620 original size:17 final size:17
Alignment explanation
Indices: 8625594--8625632 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
8625584 TCTATTCACA
*
8625594 AATTTTTAATTTAATTT
1 AATTTATAATTTAATTT
*
8625611 AATTTATAATTTTATTT
1 AATTTATAATTTAATTT
*
8625628 TATTT
1 AATTT
8625633 TCAATTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTATAATTTAATTT
Found at i:8625638 original size:17 final size:16
Alignment explanation
Indices: 8625597--8625639 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
8625587 ATTCACAAAT
8625597 TTTTAATTTAATTTAA
1 TTTTAATTTAATTTAA
* *
8625613 TTTATAATTTTATTTTA
1 TTT-TAATTTAATTTAA
8625630 TTTTCAATTT
1 TTTT-AATTT
8625640 CTTTAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTTAATTTAA
Done.