Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 60 of 206
Found at i:16962161 original size:46 final size:43
Alignment explanation
Indices: 16962110--16962196 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 43
16962100 TAAGACCTTC
*
16962110 ACATTTTGAAAAAAGAAAAATATC-ACACCCAATGCGTTAGGGCACA
1 ACATTTT-AAAAAA-AAAAA-ATCGA-ACCCAATACGTTAGGGCACA
*
16962156 ACATTTTACAAAAAAAAAATCGGAACCCAATACGTTAGGGC
1 ACATTTTAAAAAAAAAAAATC-GAACCCAATACGTTAGGGC
16962197 TCAATTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
43 3 0.08
44 21 0.57
45 6 0.16
46 7 0.19
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (43 bp):
ACATTTTAAAAAAAAAAAATCGAACCCAATACGTTAGGGCACA
Found at i:16962384 original size:14 final size:14
Alignment explanation
Indices: 16962367--16962393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16962357 ATAAACAAAT
16962367 AAATAAATCAATAA
1 AAATAAATCAATAA
16962381 AAATAAATCAATA
1 AAATAAATCAATA
16962394 GCATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAATCAATAA
Found at i:16967884 original size:27 final size:27
Alignment explanation
Indices: 16967828--16967891 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
16967818 CAAACTGATA
16967828 TAAAATGACTGTTATGCCCCCACGTGG
1 TAAAATGACTGTTATGCCCCCACGTGG
* * *
16967855 TAATATGACTGTTATGCCCCTATGCT-G
1 TAAAATGACTGTTATGCCCCCACG-TGG
16967882 TAAAATGACT
1 TAAAATGACT
16967892 ATATGCTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (27 bp):
TAAAATGACTGTTATGCCCCCACGTGG
Found at i:16969385 original size:36 final size:36
Alignment explanation
Indices: 16969291--16969408 Score: 114
Period size: 36 Copynumber: 3.3 Consensus size: 36
16969281 TTGGTTTTGA
* *
16969291 ACACTCATTTTTCAATTTTACCGA-TCAGCGCAGGAC
1 ACACTCATTTTTCGATTTTACCGACT-AGCGCAGGGC
* * * * * *
16969327 GCACTTATTTGTT-GGTTATACCGACTAGTGCTGGGC
1 ACACTCATTT-TTCGATTTTACCGACTAGCGCAGGGC
*
16969363 ACACTCATTTTTCGATTTTACCGACCAGCGCAGGGC
1 ACACTCATTTTTCGATTTTACCGACTAGCGCAGGGC
*
16969399 ACACTTATTT
1 ACACTCATTT
16969409 ATCAGTTATA
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
35 2 0.03
36 58 0.92
37 3 0.05
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (36 bp):
ACACTCATTTTTCGATTTTACCGACTAGCGCAGGGC
Found at i:16969435 original size:36 final size:36
Alignment explanation
Indices: 16969328--16969520 Score: 154
Period size: 36 Copynumber: 5.4 Consensus size: 36
16969318 GCGCAGGACG
** * * *
16969328 CACTTATTTGTTGGTTATACCGACTAGTGCTGGGCA
1 CACTTATTTGTCAGTTATACCGACCAATGTTGGGCA
* * * ** **
16969364 CACTCATTTTTC-GATTTTACCGACCAGCGCAGGGCA
1 CACTTATTTGTCAG-TTATACCGACCAATGTTGGGCA
* * *
16969400 CACTTATTTATCAGTTATACCAACCAATATTGGGCA
1 CACTTATTTGTCAGTTATACCGACCAATGTTGGGCA
* * * * ** *
16969436 CATTTATTTGTCGGTTTTACCGACCAGTGCAGGGCG
1 CACTTATTTGTCAGTTATACCGACCAATGTTGGGCA
*
16969472 CACTTATTTGTCAGTTATACTGACCAATGTTGGGCA
1 CACTTATTTGTCAGTTATACCGACCAATGTTGGGCA
*
16969508 CACTCATTTGTCA
1 CACTTATTTGTCA
16969521 ATTTTATCGG
Statistics
Matches: 120, Mismatches: 35, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
35 1 0.01
36 118 0.98
37 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (36 bp):
CACTTATTTGTCAGTTATACCGACCAATGTTGGGCA
Found at i:16969536 original size:72 final size:72
Alignment explanation
Indices: 16969291--16969526 Score: 292
Period size: 72 Copynumber: 3.3 Consensus size: 72
16969281 TTGGTTTTGA
* * * ** * *
16969291 ACACTCATTTTTCAATTTTACCGATCAGCGCAGGACGCACTTATTTGTTGGTTATACCGACTAGT
1 ACACTCATTTGTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
*
16969356 GCTGGGC
66 GTTGGGC
* * * * *
16969363 ACACTCATTTTTCGATTTTACCGACCAGCGCAGGGCACACTTATTTATCAGTTATACCAACCAAT
1 ACACTCATTTGTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
*
16969428 ATTGGGC
66 GTTGGGC
* * ** * *
16969435 ACATTTATTTGTCGGTTTTACCGACCAGTGCAGGGCGCACTTATTTGTCAGTTATACTGACCAAT
1 ACACTCATTTGTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
16969500 GTTGGGC
66 GTTGGGC
16969507 ACACTCATTTGTCAATTTTA
1 ACACTCATTTGTCAATTTTA
16969527 TCGGCCAGTG
Statistics
Matches: 138, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 138 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (72 bp):
ACACTCATTTGTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
GTTGGGC
Found at i:16975358 original size:15 final size:17
Alignment explanation
Indices: 16975338--16975374 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
16975328 CGGGGTTTAG
16975338 TTTTTTA-TCTCCA-TC
1 TTTTTTACTCTCCATTC
*
16975353 TTTTTTACTCTTCATTC
1 TTTTTTACTCTCCATTC
16975370 TTTTT
1 TTTTT
16975375 CTGTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 5 0.26
17 7 0.37
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTACTCTCCATTC
Found at i:16978342 original size:25 final size:25
Alignment explanation
Indices: 16978290--16978344 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
16978280 AACGCAATTC
*
16978290 GAACAGAACAAAATCGAATAGAGCA
1 GAACAGAACAAAATCGAACAGAGCA
* * * *
16978315 GAACAGAACAAGATGGAACATAGTA
1 GAACAGAACAAAATCGAACAGAGCA
16978340 GAACA
1 GAACA
16978345 ATACTGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.55, C:0.15, G:0.22, T:0.09
Consensus pattern (25 bp):
GAACAGAACAAAATCGAACAGAGCA
Found at i:16979428 original size:42 final size:42
Alignment explanation
Indices: 16979369--16979529 Score: 171
Period size: 42 Copynumber: 3.8 Consensus size: 42
16979359 TGAGTTACAT
* *
16979369 GGCTTGGACACACACCCATGTCCTTGCCCGTATGGCTCACAC
1 GGCTTGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
**
16979411 GGCTTGGGCACACACCCATGTCCTTGCTAGTGTGGCTCACAC
1 GGCTTGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
* * * * ** *
16979453 GG-TCTAGGCACACGCCGATATCCTTGCCCGTGTAACTCACAT
1 GGCT-TGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
* * * *
16979495 GGCCTGGGCACACGCCCATGTCCCTGGCCGTGTGG
1 GGCTTGGGCACACACCCATGTCCTTGCCCGTGTGG
16979530 TTCTAAAGCG
Statistics
Matches: 96, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
41 1 0.01
42 95 0.99
ACGTcount: A:0.17, C:0.35, G:0.26, T:0.22
Consensus pattern (42 bp):
GGCTTGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
Found at i:16979595 original size:188 final size:186
Alignment explanation
Indices: 16979275--16979639 Score: 410
Period size: 188 Copynumber: 2.0 Consensus size: 186
16979265 ACAACCTGGA
* * *
16979275 CACACGCCTATGTCCTTGCCCGTGCTCACACGGCCTGGGCACACGCCCATGTCGTCTACCTGTAT
1 CACACGCCGATATCCTTGCCCGTGCTCACACGGCCTGGGCACACGCCCATGTCGCCTACCTGTAT
** * ** * *
16979340 GGTTCTAAATTATAAACAGTGAGTTACATGGCTTGGACACACACCCATGTCCTTGCCCGTATGGC
66 GGTTCTAAAGCATAAACAGTAAGTTACACAGCCTGGACACACACCAATGTCCTTGCCCGTATGGC
* * *
16979405 TCACACGGCTTGGGCACACACCCATGTCCTTGCTAGTGTGGCTCACACGGTCTAGG
131 TCACACGGCCTGGGCACACACCCATATCCTTGCCAGTGTGGCTCACACGGTCTAGG
* *
16979461 CACACGCCGATATCCTTGCCCGTGTAACTCACATGGCCTGGGCACACGCCCATGTC-CCTGGCC-
1 CACACGCCGATATCCTTGCCCGTG---CTCACACGGCCTGGGCACACGCCCATGTCGCCT-ACCT
* * * ** ** * *
16979524 GTGTGGTTCTAAAGCGTAAATAGTAAGTTACACAGCCTGGACACACGTCAATGTCCTTTTCTGTG
62 GTATGGTTCTAAAGCATAAACAGTAAGTTACACAGCCTGGACACACACCAATGTCCTTGCCCGTA
** * ** *
16979589 TGGCTCACGTGGCCTGGGTACATGCCCATATCCTTGCCCGTGTGGCTCACA
127 TGGCTCACACGGCCTGGGCACACACCCATATCCTTGCCAGTGTGGCTCACA
16979640 TAGCCTGGGA
Statistics
Matches: 145, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
186 22 0.15
188 93 0.64
189 30 0.21
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.25
Consensus pattern (186 bp):
CACACGCCGATATCCTTGCCCGTGCTCACACGGCCTGGGCACACGCCCATGTCGCCTACCTGTAT
GGTTCTAAAGCATAAACAGTAAGTTACACAGCCTGGACACACACCAATGTCCTTGCCCGTATGGC
TCACACGGCCTGGGCACACACCCATATCCTTGCCAGTGTGGCTCACACGGTCTAGG
Found at i:16979623 original size:42 final size:42
Alignment explanation
Indices: 16979586--16979675 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
16979576 GTCCTTTTCT
* * *
16979586 GTGTGGCTCACGTGGCCTGGGTACATGCCCATATCCTTGCCC
1 GTGTGGCTCACATAGCCTGGGAACATGCCCATATCCTTGCCC
* * *
16979628 GTGTGGCTCACATAGCCTGGGAACATGCCCATGTCCCTGGCC
1 GTGTGGCTCACATAGCCTGGGAACATGCCCATATCCTTGCCC
16979670 GTGTGG
1 GTGTGG
16979676 TGTCGACAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.13, C:0.31, G:0.31, T:0.24
Consensus pattern (42 bp):
GTGTGGCTCACATAGCCTGGGAACATGCCCATATCCTTGCCC
Found at i:16980785 original size:30 final size:30
Alignment explanation
Indices: 16980724--16980785 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
16980714 GGTTGGGATG
* * **
16980724 GGAGTAAAAGTTTTGGAAGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGGAAGAAAAATAAAAA
16980754 GGAGTAAAAGTTTT-GAGAGAAAAATAAAAA
1 GGAGTAAAAGTTTTGGA-AGAAAAATAAAAA
16980784 GG
1 GG
16980786 TTTGGGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGAAGAAAAATAAAAA
Found at i:16981746 original size:39 final size:37
Alignment explanation
Indices: 16981702--16981786 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 37
16981692 ATTTTTTTAC
*
16981702 AATATTTTTCAATTTCTAATAATTTATTATAATATGTAT
1 AATATTTTTCAATTTCTAATAAATT-TTATAATAT-TAT
* *
16981741 AATATTTTACAATTTCTAATAAATTTTATAATGTTAT
1 AATATTTTTCAATTTCTAATAAATTTTATAATATTAT
*
16981778 GATATTTTT
1 AATATTTTT
16981787 ATTATTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 10 0.24
38 8 0.20
39 23 0.56
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (37 bp):
AATATTTTTCAATTTCTAATAAATTTTATAATATTAT
Found at i:16981768 original size:19 final size:19
Alignment explanation
Indices: 16981705--16981768 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
16981695 TTTTTACAAT
*
16981705 ATTTTTCAATTTCTAATAA
1 ATTTTACAATTTCTAATAA
* * * *
16981724 TTTATTATAATATGT-ATAA
1 ATT-TTACAATTTCTAATAA
16981743 TATTTTACAATTTCTAATAA
1 -ATTTTACAATTTCTAATAA
16981763 ATTTTA
1 ATTTTA
16981769 TAATGTTATG
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTTACAATTTCTAATAA
Found at i:16981863 original size:21 final size:21
Alignment explanation
Indices: 16981839--16981880 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16981829 ATATTAATAA
*
16981839 ATTTATAATTTT-TATAATTTT
1 ATTTAT-ATTTTATAAAATTTT
16981860 ATTTATATTTTATAAAATTTT
1 ATTTATATTTTATAAAATTTT
16981881 TACAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTATATTTTATAAAATTTT
Found at i:16984609 original size:2 final size:2
Alignment explanation
Indices: 16984602--16984626 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16984592 TTTTATCTAT
16984602 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 T
16984627 GTAGGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16993451 original size:107 final size:108
Alignment explanation
Indices: 16993259--16993453 Score: 284
Period size: 107 Copynumber: 1.8 Consensus size: 108
16993249 AGGGGGTGAC
* * * * *
16993259 ATTCTAGGATCTTTTGCATGTTATAAAAAATATATGTAAATGAATGTTGATGAATTATATAGTTG
1 ATTCTAAGATCTTTTGCATGTTATAAAAAATACATCTAAATGAATGATGATGAATTATATAATTG
* * *
16993324 TTATTATGTAATTTTGTCAAGGTGTACCTAAAATTAGAACAAT
66 TTATTAGGTAATGTTATCAAGGTGTACCTAAAATTAGAACAAT
** *
16993367 ATTCTAAGATCTTTTGCATGTTAT-TGAAATACATCTAAATGGATGATGATGAATTATATAATTG
1 ATTCTAAGATCTTTTGCATGTTATAAAAAATACATCTAAATGAATGATGATGAATTATATAATTG
16993431 TTATTAGGTAATGTTATCAAGGT
66 TTATTAGGTAATGTTATCAAGGT
16993454 TGTAGTTACA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
107 53 0.70
108 23 0.30
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (108 bp):
ATTCTAAGATCTTTTGCATGTTATAAAAAATACATCTAAATGAATGATGATGAATTATATAATTG
TTATTAGGTAATGTTATCAAGGTGTACCTAAAATTAGAACAAT
Found at i:16996754 original size:18 final size:17
Alignment explanation
Indices: 16996733--16996776 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
16996723 TATTTATTTA
16996733 TTTTAATTTTAACATAAT
1 TTTTAATTTTAA-ATAAT
*
16996751 TTTTATATTTTAAATTAT
1 TTTTA-ATTTTAAATAAT
*
16996769 TATTAATT
1 TTTTAATT
16996777 ATCACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAATTTTAAATAAT
Found at i:16996818 original size:17 final size:16
Alignment explanation
Indices: 16996796--16996836 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
16996786 ATAGTTTTAA
16996796 TTATTTAATTTAGATTT
1 TTATTTAATTTA-ATTT
*
16996813 TTATTTTATTTTAATTT
1 TTA-TTTAATTTAATTT
16996830 TTATTTA
1 TTATTTA
16996837 CCAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTAATTTAATTT
Found at i:16998911 original size:24 final size:24
Alignment explanation
Indices: 16998884--16998929 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
16998874 GTTCAAACAA
*
16998884 TATATAATTTTAATTATAAAAATT
1 TATATAAATTTAATTATAAAAATT
16998908 TATATAAATTTAATTATAAAAA
1 TATATAAATTTAATTATAAAAA
16998930 GACTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATATAAATTTAATTATAAAAATT
Found at i:16998937 original size:24 final size:24
Alignment explanation
Indices: 16998884--16998938 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
16998874 GTTCAAACAA
* **
16998884 TATATAATTTTAATTATAAAAATT
1 TATATAAATTTAATTATAAAAAAC
16998908 TATATAAATTTAATTATAAAAAGAC
1 TATATAAATTTAATTATAAAAA-AC
16998933 TTATAT
1 -TATAT
16998939 TAACTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
26 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TATATAAATTTAATTATAAAAAAC
Found at i:16999379 original size:22 final size:22
Alignment explanation
Indices: 16999354--16999445 Score: 103
Period size: 22 Copynumber: 4.2 Consensus size: 22
16999344 AAATTCAATA
* *
16999354 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* * *
16999376 TCAATTCCTTTTAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
16999398 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
16999420 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
16999442 TCAA
1 TCAA
16999446 ACTCTCAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.43
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:16999411 original size:44 final size:44
Alignment explanation
Indices: 16999354--16999445 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
16999344 AAATTCAATA
* * * **
16999354 TCAATTTCTTTCAAAAATTCTCTCAA-TTCCTTTTAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTATCAATTTCCTTCCAAAA-TTCTC
*
16999398 TCAATTCCCTTCAAAATTTCTATCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTATCAATTTCCTTCCAAAATTCTC
16999442 TCAA
1 TCAA
16999446 ACTCTCAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 31 0.76
45 10 0.24
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.43
Consensus pattern (44 bp):
TCAATTCCCTTCAAAAATTCTATCAATTTCCTTCCAAAATTCTC
Found at i:17012124 original size:4 final size:4
Alignment explanation
Indices: 17012115--17012140 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17012105 AGTAAGCAAT
17012115 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
17012141 GTGTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:17029039 original size:5 final size:5
Alignment explanation
Indices: 17029029--17029067 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
17029019 GTCTAAGATG
* *
17029029 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
17029068 GCTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:17029264 original size:22 final size:22
Alignment explanation
Indices: 17029202--17029253 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
17029192 TAAGAATCTA
*
17029202 TATGTGTTAATTGAATTGTATG
1 TATGTGTTAATTTAATTGTATG
17029224 TATGTGTTAATTTAATTGTATG
1 TATGTGTTAATTTAATTGTATG
17029246 TATGTGTT
1 TATGTGTT
17029254 TGTATTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (22 bp):
TATGTGTTAATTTAATTGTATG
Found at i:17029562 original size:26 final size:25
Alignment explanation
Indices: 17029532--17029606 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
17029522 ATTACTCTTA
*
17029532 TGAGCGTCCTGTTATATGGCTCTTCG
1 TGAGCTTCCTGTTA-ATGGCTCTTCG
* * *
17029558 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCTG-TTAATGGCTCTTCG
*
17029584 TGAGCTTCCTAATTAATGGCTCT
1 TGAGCTTCCT-GTTAATGGCTCT
17029607 CTAAAGCTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 37 0.93
27 3 0.08
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (25 bp):
TGAGCTTCCTGTTAATGGCTCTTCG
Found at i:17029627 original size:23 final size:24
Alignment explanation
Indices: 17029599--17029664 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
17029589 TTCCTAATTA
*
17029599 ATGGCTCTCTAAAGCTTCTCG-AT
1 ATGGCTCTCTGAAGCTTCTCGAAT
*
17029622 ATGGCTCGCTTGAA-CTTCTCGATAT
1 ATGGCTCTC-TGAAGCTTCTCGA-AT
*
17029647 ATGGCTATCTGAAGCTTC
1 ATGGCTCTCTGAAGCTTC
17029665 CCGTTAATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 15 0.43
24 7 0.20
25 13 0.37
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (24 bp):
ATGGCTCTCTGAAGCTTCTCGAAT
Found at i:17029686 original size:24 final size:24
Alignment explanation
Indices: 17029659--17029742 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
17029649 GGCTATCTGA
*
17029659 AGCTTCCCGTTAATGGCTCG-TTGG
1 AGCTTCCCGTTAATGGCTCGCAT-G
* * *
17029683 AGCTACTCGTTATTGGCTCGCATG
1 AGCTTCCCGTTAATGGCTCGCATG
* ***
17029707 AGCTTCCCGTTTATGGCTATTATG
1 AGCTTCCCGTTAATGGCTCGCATG
*
17029731 AGCTTCCTGTTA
1 AGCTTCCCGTTA
17029743 TACAGCCCAG
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
24 45 0.98
25 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (24 bp):
AGCTTCCCGTTAATGGCTCGCATG
Found at i:17029700 original size:48 final size:48
Alignment explanation
Indices: 17029599--17029724 Score: 123
Period size: 48 Copynumber: 2.6 Consensus size: 48
17029589 TTCCTAATTA
* * * *
17029599 ATGGCTCTCTAAAGCTTCTCGATATGGCTCGCTTGAACTTCTCGATAT
1 ATGGCTCTCTGAAGCTTCCCGTTATGGCTCGCTTGAACTACTCGATAT
* * *
17029647 ATGGCTATCTGAAGCTTCCCGTTAATGGCTCG-TTGGAGCTACTCGTTAT
1 ATGGCTCTCTGAAGCTTCCCGTT-ATGGCTCGCTT-GAACTACTCGATAT
*
17029696 -TGGCTCGCATG-AGCTTCCCGTTTATGGCT
1 ATGGCTCTC-TGAAGCTTCCCG-TTATGGCT
17029725 ATTATGAGCT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
48 42 0.65
49 23 0.35
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (48 bp):
ATGGCTCTCTGAAGCTTCCCGTTATGGCTCGCTTGAACTACTCGATAT
Found at i:17032983 original size:2 final size:2
Alignment explanation
Indices: 17032976--17033001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17032966 ACATGAATTA
17032976 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
17033002 GAATGTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17034158 original size:23 final size:22
Alignment explanation
Indices: 17034128--17034172 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17034118 AAATTAAATC
17034128 TCTAAGATTACAAAATCTTATCT
1 TCTAAGATTAC-AAATCTTATCT
* *
17034151 TCTAAGATTGCATATCTTATCT
1 TCTAAGATTACAAATCTTATCT
17034173 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTAAGATTACAAATCTTATCT
Found at i:17034195 original size:17 final size:19
Alignment explanation
Indices: 17034154--17034195 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17034144 CTTATCTTCT
* *
17034154 AAGATTGCATATCTTATCT
1 AAGATTGCATATCCTATCG
17034173 AAGATTGCATATCCT-T-G
1 AAGATTGCATATCCTATCG
17034190 AAGATT
1 AAGATT
17034196 ATGTTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 14 0.67
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (19 bp):
AAGATTGCATATCCTATCG
Found at i:17034946 original size:51 final size:51
Alignment explanation
Indices: 17034877--17034997 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
17034867 ATCTACTATG
* * * * * *
17034877 ACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTCAATTTATTCCACTGCA
1 ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAATCTATACCACTGCA
*
17034928 ACGCCAAGGAAATGAGATTCGTTGCCCTCAACTTCAATCTATACCACTGCA
1 ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAATCTATACCACTGCA
17034979 ACGCCAAGGAAATGAGATT
1 ACGCCAAGGAAATGAGATT
17034998 GGTGTCTTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (51 bp):
ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAATCTATACCACTGCA
Found at i:17035232 original size:19 final size:19
Alignment explanation
Indices: 17035208--17035261 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
17035198 AATATTTTCT
*
17035208 TCTAAGATTGCATATCTTA
1 TCTAAGATTGCATATCATA
17035227 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
17035246 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
17035262 CTTAAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:17041741 original size:69 final size:68
Alignment explanation
Indices: 17041617--17041983 Score: 322
Period size: 69 Copynumber: 5.3 Consensus size: 68
17041607 TTTAGAATTT
* ** * * * * * *
17041617 TTCGTCTGCGAACCTTGATCATACAGTTGGGAGCTTTGCTTTTGCTGACTGTTTTGGAGGTTGCA
1 TTCGCCTGCGAACCTTGATTTTACAGTTGGGAGCTTTACTCTCGCTAACTATTTTGGAGGTCGCA
* *
17041682 TTTT
66 -CTC
* * * *
17041686 TTCGCCTGTGAACCTTGATTTTATAGTTGGAAACTTTACTCTCGCTAACTATTTTGGAGGTCGCG
1 TTCGCCTGCGAACCTTGATTTTACAGTTGGGAGCTTTACTCTCGCTAACTATTTTGGAGGTCGC-
17041751 ACTC
65 ACTC
* * * *
17041755 TTCACTTGCGAACCTTGATTTTACAGTTGGGAGTTTTACTCTCGCTAACTGTTTTGGAGGTCGCC
1 TTCGCCTGCGAACCTTGATTTTACAGTTGGGAGCTTTACTCTCGCTAACTATTTTGGAGGTCG-C
*
17041820 GCTC
65 ACTC
* * *
17041824 TTCGCCTGCGAACCTTGATTTTATAGCTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCATG
1 TTCGCCTGCGAACCTTGATTTTACAGTTGGGAGCTTTACTCTCGCTAACTATTTTGGAGGTC--G
*
17041889 -GCTC
64 CACTC
* ** * * * * * * * *
17041893 TTCGCCTGCAAACCTTGATTTTTGAGCTCGGAGCTTTGCTTTCACTAATTGTTTTAGAGGTCGCG
1 TTCGCCTGCGAACCTTGATTTTACAGTTGGGAGCTTTACTCTCGCTAACTATTTTGGAGGTCGC-
*
17041958 GCTC
65 ACTC
* **
17041962 TTTGCCTATGAACCTTGATTTT
1 TTCGCCTGCGAACCTTGATTTT
17041984 TCTATGATAA
Statistics
Matches: 248, Mismatches: 44, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
67 1 0.00
69 244 0.98
70 2 0.01
71 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (68 bp):
TTCGCCTGCGAACCTTGATTTTACAGTTGGGAGCTTTACTCTCGCTAACTATTTTGGAGGTCGCA
CTC
Found at i:17041786 original size:138 final size:138
Alignment explanation
Indices: 17041622--17041983 Score: 418
Period size: 138 Copynumber: 2.6 Consensus size: 138
17041612 AATTTTTCGT
** * * * ** *
17041622 CTGCGAACCTTGATCATACAGTTGGGAGCTTTGCTTTTGCTGACTGTTTTGGAGGTTGCATTTTT
1 CTGCGAACCTTGATTTTACAGTTGGGAGCTTTGCTTTCGCTAACTGTTTTGGAGGTCGCAGCTCT
* * *
17041687 TCGCCTGTGAACCTTGATTTTATAGTTGGAAACTTTACTCTCGCTAACTATTTTGGAGGTCGCGA
66 TCGCCTGCGAACCTTGATTTTATAGCTGGAAACTTTACTCTCGCTAACTATTTTGGAGGTCACGA
17041752 CTCTTCAC
131 CTCTTCAC
* * * * *
17041760 TTGCGAACCTTGATTTTACAGTTGGGAGTTTTACTCTCGCTAACTGTTTTGGAGGTCGCCGCTCT
1 CTGCGAACCTTGATTTTACAGTTGGGAGCTTTGCTTTCGCTAACTGTTTTGGAGGTCGCAGCTCT
* * * * *
17041825 TCGCCTGCGAACCTTGATTTTATAGCTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTCATGG
66 TCGCCTGCGAACCTTGATTTTATAGCTGGAAACTTTACTCTCGCTAACTATTTTGGAGGTCACGA
*
17041890 CTCTTCGC
131 CTCTTCAC
* ** * * * * * *
17041898 CTGCAAACCTTGATTTTTGAGCTCGGAGCTTTGCTTTCACTAATTGTTTTAGAGGTCGCGGCTCT
1 CTGCGAACCTTGATTTTACAGTTGGGAGCTTTGCTTTCGCTAACTGTTTTGGAGGTCGCAGCTCT
* **
17041963 TTGCCTATGAACCTTGATTTT
66 TCGCCTGCGAACCTTGATTTT
17041984 TCTATGATAA
Statistics
Matches: 186, Mismatches: 38, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
138 186 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (138 bp):
CTGCGAACCTTGATTTTACAGTTGGGAGCTTTGCTTTCGCTAACTGTTTTGGAGGTCGCAGCTCT
TCGCCTGCGAACCTTGATTTTATAGCTGGAAACTTTACTCTCGCTAACTATTTTGGAGGTCACGA
CTCTTCAC
Found at i:17046861 original size:19 final size:20
Alignment explanation
Indices: 17046839--17046879 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
17046829 AATTTCTTAA
*
17046839 TATTATTATCCCAT-AACAT
1 TATTATAATCCCATAAACAT
17046858 TATTATAATCCCATAAACAT
1 TATTATAATCCCATAAACAT
17046878 TA
1 TA
17046880 AATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (20 bp):
TATTATAATCCCATAAACAT
Found at i:17046884 original size:19 final size:19
Alignment explanation
Indices: 17046846--17046885 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17046836 TAATATTATT
*
17046846 ATCCCATAACATTATTATA
1 ATCCCATAACATTATAATA
17046865 ATCCCATAAACATTA-AATA
1 ATCCCAT-AACATTATAATA
17046884 AT
1 AT
17046886 AAAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCCCATAACATTATAATA
Found at i:17065905 original size:139 final size:139
Alignment explanation
Indices: 17065722--17066204 Score: 390
Period size: 129 Copynumber: 3.5 Consensus size: 139
17065712 CCTTTCCTAC
* * * *
17065722 TCATATTTATATTTTTTTATTTCATGTTGCTTTAAGCTTTTTAAAATTTTAATTAA-ATTTGTTA
1 TCATATTTGTA-TTTTTTATTTCATGTTGCTTCAACCTTTTTAAATTTTTAATTAATATTT-TTA
* *
17065786 TCATATTAGTTCTTTGGTTAGATAGTTAGATAATTGTAATTATATCCTTGAGTCTCAAGTTTAAT
64 ACATATTAGTTCTTTGGTTAGATAGTTAGATAATTGTAATTATATCCTTGAGTCTCAAGTTCAAT
* *
17065851 T-TCTCTCCTAT
129 TCT-TCTACTAA
* * * *
17065862 TTATATTTGTATTTTTTATTTCATGTTACTTCATCCTTTTTAAATTTTTAATTAATGTTTTTTAA
1 TCATATTTGTATTTTTTATTTCATGTTGCTTCAACCTTTTTAAATTTTTAATTAAT-ATTTTTAA
* * * * *
17065927 CATTTTAGTTTTTTGCCTTAGATGGTTAG---A-TGTAA-T-TA--C---A-TCTCAAGTTCGAT
65 CATATTAGTTCTTTG-GTTAGATAGTTAGATAATTGTAATTATATCCTTGAGTCTCAAGTTCAAT
*
17065980 TCTTTTACTAA
129 TCTTCTACTAA
* * **
17065991 TCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCATTTTTTTTATTTTTAATTAATATTTTTA
1 TCATATTTGTATTTTTTATTTCATGTTGCTTCAA-C-CTTTTTAAATTTTTAATTAATATTTTTA
* * * * * * *
17066056 GCATGTTAGTTCATTTCGTTAGATAGTTAGATAATTGTGATTACATCCTTGAGTCTGAGGTTCAA
64 ACATATTAGTTC-TTTGGTTAGATAGTTAGATAATTGTAATTATATCCTTGAGTCTCAAGTTCAA
* *
17066121 TTATTTTTA-TAA
128 TT-CTTCTACTAA
* * * * * *
17066133 GCATATTAATGTATTTTTAATTTCATATTGTTTCAAACTTTTT-TATTTTTAATT-AT-TTTTAT
1 TCATATT--TGTATTTTTTATTTCATGTTGCTTCAACCTTTTTAAATTTTTAATTAATATTTT-T
17066195 AAGCATATTA
63 AA-CATATTA
17066205 TTATTATTTT
Statistics
Matches: 272, Mismatches: 47, Indels: 47
0.74 0.13 0.13
Matches are distributed among these distances:
129 47 0.17
130 29 0.11
131 21 0.08
133 2 0.01
134 4 0.01
135 3 0.01
136 2 0.01
137 5 0.02
138 2 0.01
139 43 0.16
140 29 0.11
141 32 0.12
142 24 0.09
143 5 0.02
144 24 0.09
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (139 bp):
TCATATTTGTATTTTTTATTTCATGTTGCTTCAACCTTTTTAAATTTTTAATTAATATTTTTAAC
ATATTAGTTCTTTGGTTAGATAGTTAGATAATTGTAATTATATCCTTGAGTCTCAAGTTCAATTC
TTCTACTAA
Found at i:17072161 original size:23 final size:23
Alignment explanation
Indices: 17072091--17072171 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 23
17072081 CCTGATCAGT
*
17072091 ATACGACACAT-AAGTGTCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
17072112 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
17072132 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
17072155 ATACGACACATAAAGTG
1 ATACGACACATAAAGTG
17072172 TCTAATCGGC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 9 0.18
21 22 0.45
23 18 0.37
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:17077700 original size:22 final size:21
Alignment explanation
Indices: 17077655--17077697 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
17077645 TAAGGTAAGT
17077655 TTATAAAAATTAATATATAAA
1 TTATAAAAATTAATATATAAA
17077676 TTATAAATAATATAATTATATA
1 TTATAAA-AAT-TAA-TATATA
17077698 TTAAAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 3 0.16
24 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATAAAAATTAATATATAAA
Found at i:17086823 original size:17 final size:17
Alignment explanation
Indices: 17086798--17086832 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17086788 TTAAAACTCT
*
17086798 AACGGAAACTGTTAATC
1 AACGAAAACTGTTAATC
17086815 AACGAAAACTGTTAATC
1 AACGAAAACTGTTAATC
17086832 A
1 A
17086833 GCCACTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (17 bp):
AACGAAAACTGTTAATC
Found at i:17089560 original size:32 final size:32
Alignment explanation
Indices: 17089519--17089582 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
17089509 TATACGTAAA
17089519 ATTAAAAGATTATACATACACCAACAATGTTT
1 ATTAAAAGATTATACATACACCAACAATGTTT
17089551 ATTAAAAGATTATACATACACCAACAATGTTT
1 ATTAAAAGATTATACATACACCAACAATGTTT
17089583 TTTAGGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (32 bp):
ATTAAAAGATTATACATACACCAACAATGTTT
Found at i:17089615 original size:51 final size:52
Alignment explanation
Indices: 17089559--17089656 Score: 173
Period size: 51 Copynumber: 1.9 Consensus size: 52
17089549 TTATTAAAAG
17089559 ATTATACATACACCAACAATGTTTTTTAGGGTA-AATAAC-ATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGG-ACAATAACAATTAAACCAACA
17089610 ATTATACATACACCAACAATGTTTTTTAGGGACAATAACAATTAAAC
1 ATTATACATACACCAACAATGTTTTTTAGGGACAATAACAATTAAAC
17089657 ATTATCCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 1 0.02
51 37 0.82
52 7 0.16
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (52 bp):
ATTATACATACACCAACAATGTTTTTTAGGGACAATAACAATTAAACCAACA
Found at i:17089684 original size:18 final size:18
Alignment explanation
Indices: 17089657--17089694 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17089647 ACAATTAAAC
* *
17089657 ATTATCCATACATCAACA
1 ATTATACATACACCAACA
17089675 ATTATACATACACCAACA
1 ATTATACATACACCAACA
17089693 AT
1 AT
17089695 GTTTTTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTATACATACACCAACA
Found at i:17089756 original size:33 final size:33
Alignment explanation
Indices: 17089719--17089782 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
17089709 ATAACATTAA
** *
17089719 ACCAACAAGTAATTTTAGGTCAATTGTACATAC
1 ACCAACAAGTAATGCTAGGTCAATTATACATAC
*
17089752 ACCAACAATTAATGCTAGGTCAATTATACAT
1 ACCAACAAGTAATGCTAGGTCAATTATACAT
17089783 GCTTTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (33 bp):
ACCAACAAGTAATGCTAGGTCAATTATACATAC
Found at i:17092882 original size:29 final size:28
Alignment explanation
Indices: 17092848--17092934 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
17092838 TCATAAGGAC
17092848 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
17092877 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
17092901 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
17092931 ATTT
1 ATTT
17092935 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:17093148 original size:143 final size:144
Alignment explanation
Indices: 17092991--17093420 Score: 560
Period size: 143 Copynumber: 2.9 Consensus size: 144
17092981 TAAGAATATG
* * *
17092991 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAAAAATTATGTTTA
* * *
17093056 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAT
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
17093121 AACAAATTTCTGCT
131 AACAAATTTCTGCT
****
17093135 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAAAAATTATGTTTA
*
17093199 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAAT
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAAC---
*
17093264 AATCATTTACCAAAATAATTTTTTGCT
128 AAT-A---A-C---A-AA-TTTCTGCT
**** * *
17093291 AATTA-TAAGAATTTTATTAAATTATATATTTTAATT-AAATATATTTAATTATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAAAAATTATGTTTA
17093354 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
17093419 AA
131 AA
17093421 TCATTTACCA
Statistics
Matches: 258, Mismatches: 15, Indels: 22
0.87 0.05 0.07
Matches are distributed among these distances:
143 110 0.43
144 5 0.02
146 3 0.01
147 1 0.00
148 1 0.00
150 1 0.00
151 2 0.01
152 3 0.01
154 1 0.00
155 88 0.34
156 43 0.17
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (144 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAAAAATTATGTTTA
AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
AACAAATTTCTGCT
Found at i:17093173 original size:18 final size:17
Alignment explanation
Indices: 17093145--17093179 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17093135 AATTATAAGA
*
17093145 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17093162 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17093180 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17093179 original size:16 final size:16
Alignment explanation
Indices: 17093145--17093199 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
17093135 AATTATAAGA
17093145 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
17093162 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
17093178 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
17093192 ATGTTTAA
1 AT-TTTAA
17093200 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:17093323 original size:17 final size:17
Alignment explanation
Indices: 17093301--17093334 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17093291 AATTATAAGA
17093301 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
17093318 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
17093335 TTAATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:17093324 original size:14 final size:14
Alignment explanation
Indices: 17093305--17093343 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
17093295 ATAAGAATTT
*
17093305 TATTAAATTATATA
1 TATTTAATTATATA
*
17093319 T-TTTAATTAAATA
1 TATTTAATTATATA
17093332 TATTTAATTATA
1 TATTTAATTATA
17093344 ATTATGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTAATTATATA
Found at i:17093334 original size:15 final size:16
Alignment explanation
Indices: 17093314--17093354 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
17093304 TTATTAAATT
17093314 ATATATTTTAATTA-A
1 ATATATTTTAATTATA
17093329 ATATA-TTTAATTATA
1 ATATATTTTAATTATA
17093344 AT-TATGTTTAA
1 ATATAT-TTTAA
17093355 ATATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.43
15 8 0.35
16 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:17093364 original size:155 final size:156
Alignment explanation
Indices: 17093121--17093440 Score: 570
Period size: 155 Copynumber: 2.1 Consensus size: 156
17093111 CAATAACAAT
* *
17093121 AACAAATTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
1 AACAATTTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
17093186 AAAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 AAAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
*
17093251 TAACATTAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
* *
17093277 AATAATTTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATT-AAATATATTTAATT
1 AACAATTTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
*
17093341 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 AAAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
17093406 TAACAATAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
17093432 CACAATTTT
1 AACAATTTT
17093441 ATACTAAGGG
Statistics
Matches: 156, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
155 109 0.70
156 47 0.30
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (156 bp):
AACAATTTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
AAAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
TAACAATAACAATAATCATTTACCAA
Found at i:17093592 original size:16 final size:16
Alignment explanation
Indices: 17093571--17093606 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17093561 GAATAGCTAT
17093571 TACACCTCTAATCAAA
1 TACACCTCTAATCAAA
*
17093587 TACACCTCTAATCCAA
1 TACACCTCTAATCAAA
17093603 TACA
1 TACA
17093607 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCAAA
Found at i:17099934 original size:50 final size:50
Alignment explanation
Indices: 17099826--17100068 Score: 301
Period size: 50 Copynumber: 4.7 Consensus size: 50
17099816 GGGAATGAGA
*
17099826 TCCCATGTAAAACCATGTCTAGGACATGGCATTGGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-CC--GAGA-C--GAGAGG
*
17099882 TCCCATGTAAGACCATGTCT-GGTACATGGCGTTGGCACCGAGACGAGAGG
1 TCCCATGTAAGACCATGTCTAGG-ACATGGCATTGGCACCGAGACGAGAGG
*
17099932 TCCCATGTAAGACCATGTCT-GAGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTAG-GACATGGCATTGGCACCGAGACGAGAGG
* * * * **
17099982 TCCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGACGAGAGG
* *
17100032 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA
17100069 GTACTTGAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
50 128 0.75
51 2 0.01
52 1 0.01
53 4 0.02
55 4 0.02
56 32 0.19
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGACGAGAGG
Found at i:17103643 original size:13 final size:13
Alignment explanation
Indices: 17103625--17103649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17103615 ATTTACAAGA
17103625 TTACATAATCAAT
1 TTACATAATCAAT
17103638 TTACATAATCAA
1 TTACATAATCAA
17103650 ATCAAATCCA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:17107482 original size:13 final size:13
Alignment explanation
Indices: 17107466--17107495 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
17107456 ATTGTCATGT
17107466 AATTGTTTTTCTG
1 AATTGTTTTTCTG
17107479 AATTGTTTTTCTG
1 AATTGTTTTTCTG
17107492 AATT
1 AATT
17107496 TAGCTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (13 bp):
AATTGTTTTTCTG
Found at i:17108430 original size:18 final size:17
Alignment explanation
Indices: 17108402--17108436 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17108392 ATTATTAAGA
*
17108402 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17108419 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17108437 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17108693 original size:16 final size:16
Alignment explanation
Indices: 17108672--17108709 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
17108662 GATTTGCTAT
17108672 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17108688 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17108704 TACACC
1 TACACC
17108710 GAACCAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17109586 original size:20 final size:20
Alignment explanation
Indices: 17109563--17109604 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17109553 CAAGTAAAAA
17109563 TATAACAATAACA-ATAATAC
1 TATAACAATAA-ATATAATAC
17109583 TATAACAATAAATATAATAC
1 TATAACAATAAATATAATAC
17109603 TA
1 TA
17109605 ATGAATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAACAATAAATATAATAC
Found at i:17112376 original size:19 final size:19
Alignment explanation
Indices: 17112352--17112388 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17112342 TGATCAAGTA
17112352 AAATTAAACTAA-ATTAATC
1 AAATTAAA-TAATATTAATC
17112371 AAATTAAATAATATTAAT
1 AAATTAAATAATATTAAT
17112389 ATGATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATTAAATAATATTAATC
Found at i:17112834 original size:20 final size:19
Alignment explanation
Indices: 17112809--17112858 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
17112799 TAATAGTATT
17112809 TTATTAATTTAATATTAAA
1 TTATTAATTTAATATTAAA
17112828 GTTATT-ATCTTAATATTAAA
1 -TTATTAAT-TTAATATTAAA
17112848 -T-TTAATTTAAT
1 TTATTAATTTAAT
17112859 GTTTATCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.25
18 3 0.11
19 2 0.07
20 16 0.57
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATTAATTTAATATTAAA
Found at i:17112917 original size:12 final size:12
Alignment explanation
Indices: 17112900--17112946 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
17112890 TTTTAAAAAG
17112900 ATTTAATATTAA
1 ATTTAATATTAA
*
17112912 ATTTAAT-CTAA
1 ATTTAATATTAA
17112923 TATTT-ATATT-A
1 -ATTTAATATTAA
17112934 ATTTAATATTAA
1 ATTTAATATTAA
17112946 A
1 A
17112947 GTGATTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
11 11 0.38
12 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:17112925 original size:17 final size:18
Alignment explanation
Indices: 17112903--17112946 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
17112893 TAAAAAGATT
17112903 TAATATTAAAT-TTAATC
1 TAATATTAAATATTAATC
* *
17112920 TAATATT-TATATTAATT
1 TAATATTAAATATTAATC
17112937 TAATATTAAA
1 TAATATTAAA
17112947 GTGATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTAAATATTAATC
Found at i:17128297 original size:29 final size:30
Alignment explanation
Indices: 17128226--17128333 Score: 128
Period size: 30 Copynumber: 3.6 Consensus size: 30
17128216 TCTAATTTCC
** *
17128226 TAAAATTACATTTTGACCCCCAAACTTTTC
1 TAAAATTACATTTTGACCCCTTAACTTTTT
* *
17128256 TAAAATTATATTTTGACTCCTTAA-TTTTT
1 TAAAATTACATTTTGACCCCTTAACTTTTT
* *
17128285 TAAAATTACATTTTAACCCCTTAACTTTCT
1 TAAAATTACATTTTGACCCCTTAACTTTTT
* *
17128315 TAAAGTTGCATTTTGACCC
1 TAAAATTACATTTTGACCC
17128334 TAGAAGTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 25 0.38
30 40 0.62
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAAATTACATTTTGACCCCTTAACTTTTT
Found at i:17139484 original size:75 final size:75
Alignment explanation
Indices: 17139395--17139936 Score: 849
Period size: 75 Copynumber: 7.2 Consensus size: 75
17139385 ACCATTTCTT
* * * * *
17139395 TTTCTATTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCACAAGTTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
17139460 GTATTTTCAA
66 GTATTTTCAA
* * * *
17139470 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTG-GTTTGAGCCTTGGGTCTCAGGCTGA
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAG-TTGAGCCTCGGGTCGCACGCTGA
17139534 GGTATTTTCAA
65 GGTATTTTCAA
*
17139545 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTAAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
17139610 GTATTTTCAA
66 GTATTTTCAA
*
17139620 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTAGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
17139685 GTATTTTCAA
66 GTATTTTCAA
* *
17139695 GTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTG-GTTTGAGCCTCGGGTCGCACGCTGA
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAG-TTGAGCCTCGGGTCGCACGCTGA
17139759 GGTACTTTT-AA
65 GGTA-TTTTCAA
*
17139770 TTTCTGTTTTTCAAAAATTAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
17139835 GTATTTTCAT
66 GTATTTTCAA
* *
17139845 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTTGCACGCCGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
17139910 GTGTTTTCAA
66 GTATTTTCAA
* *
17139920 GTTC-CTTTTTCAAAAAT
1 TTTCTGTTTTTCAAAAAT
17139937 TTTTTTTTGG
Statistics
Matches: 435, Mismatches: 26, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
74 18 0.04
75 411 0.94
76 6 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (75 bp):
TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
GTATTTTCAA
Found at i:17140263 original size:29 final size:29
Alignment explanation
Indices: 17140214--17140322 Score: 121
Period size: 30 Copynumber: 3.7 Consensus size: 29
17140204 AATACAAAAT
* *
17140214 TTAAAATTTAAATTTTGACCCCTAACTTTC
1 TTAAAA-TTACATTTTAACCCCTAACTTTC
* *
17140244 TTAAAATTACATTTTAACCCTTAAACTTTT
1 TTAAAATTACATTTTAACCCCT-AACTTTC
17140274 TTAAAATTACATTTTAATCCCCTAAC-TTC
1 TTAAAATTACATTTTAA-CCCCTAACTTTC
* * *
17140303 CTAAAATTGCACTTTAACCC
1 TTAAAATTACATTTTAACCC
17140323 TAAAAGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.04
29 29 0.43
30 32 0.47
31 4 0.06
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (29 bp):
TTAAAATTACATTTTAACCCCTAACTTTC
Found at i:17140321 original size:59 final size:60
Alignment explanation
Indices: 17140213--17140332 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 60
17140203 AAATACAAAA
* * * *
17140213 TTTAAAATTTAAATTTTGACCCCTAACTTTCTTAAAATTACATTTTAACCCTTAAACTTT
1 TTTAAAATTTAAATTTTAACCCCTAACTTTCCTAAAATTACACTTTAACCCTAAAACTTT
* * *
17140273 TTTAAAA-TTACATTTTAATCCCCTAAC-TTCCTAAAATTGCACTTTAACCCTAAAAGTTT
1 TTTAAAATTTAAATTTTAA-CCCCTAACTTTCCTAAAATTACACTTTAACCCTAAAACTTT
17140332 T
1 T
17140333 ACACCCTTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 37 0.71
60 15 0.29
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (60 bp):
TTTAAAATTTAAATTTTAACCCCTAACTTTCCTAAAATTACACTTTAACCCTAAAACTTT
Found at i:17140865 original size:24 final size:24
Alignment explanation
Indices: 17140831--17140885 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
17140821 AACGAGAAGG
*
17140831 AAAAAAGGAGAAAGAA-AGGAGAA
1 AAAAAAGGAGAAAGAAGAGAAGAA
17140854 AAAAAAGAGAGAAAGAAGAGAAGAA
1 AAAAAAG-GAGAAAGAAGAGAAGAA
17140879 AAGAAAA
1 AA-AAAA
17140886 AAAAAATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.25
24 9 0.32
25 8 0.29
26 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AAAAAAGGAGAAAGAAGAGAAGAA
Found at i:17140866 original size:20 final size:21
Alignment explanation
Indices: 17140831--17140882 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
17140821 AACGAGAAGG
17140831 AAAAAAG-GAGAAAGAAAGGAGAA
1 AAAAAAGAGAGAAAG-AA-GAG-A
17140854 AAAAAAGAGAGAAAGAAGAGA
1 AAAAAAGAGAGAAAGAAGAGA
*
17140875 AGAAAAGA
1 AAAAAAGA
17140883 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
22 3 0.11
23 9 0.33
24 7 0.26
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
AAAAAAGAGAGAAAGAAGAGA
Found at i:17141009 original size:1 final size:1
Alignment explanation
Indices: 17140998--17141064 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
17140988 AAGAAGGAGC
* * * * * * * * *
17140998 AAAAAAGAAAAAAAAAGAAAAAAAAGAAAGAAGAAAGAAAAAAGAAAAAGAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17141063 AA
1 AA
17141065 GGATAGGTCG
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:17141010 original size:7 final size:7
Alignment explanation
Indices: 17141008--17141061 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
17140998 AAAAAAGAAA
17141008 AAAAAAG
1 AAAAAAG
17141015 AAAAAA-
1 AAAAAAG
*
17141021 AAGAAAG
1 AAAAAAG
*
17141028 AAGAAAG
1 AAAAAAG
17141035 AAAAAAG
1 AAAAAAG
17141042 -AAAAAG
1 AAAAAAG
17141048 AAAAAAAG
1 -AAAAAAG
17141056 AAAAAA
1 AAAAAA
17141062 AAAGGATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 11 0.26
7 25 0.60
8 6 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17141011 original size:8 final size:8
Alignment explanation
Indices: 17141007--17141062 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
17140997 CAAAAAAGAA
17141007 AAAAAAAG
1 AAAAAAAG
17141015 AAAAAAA-
1 AAAAAAAG
*
17141022 AGAAAGAAG
1 A-AAAAAAG
17141031 AAAGAAAA-
1 AAA-AAAAG
17141039 AAGAAAAAG
1 AA-AAAAAG
17141048 AAAAAAAG
1 AAAAAAAG
17141056 AAAAAAA
1 AAAAAAA
17141063 AAGGATAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 1 0.02
8 33 0.80
9 7 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:17149582 original size:44 final size:45
Alignment explanation
Indices: 17149528--17149633 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
17149518 GATAATGTGT
*
17149528 TTGCAAAACTGAGAAGAT-ATAAGAA-AAGGAAAACACGTAGATAC
1 TTGCAAAACTGAGAAGATAATAAGAACAA-GAAAACACATAGATAC
* **
17149572 TTGCAGAACTGAGAAGATAATAAGAACAAGAAAACACATAGATGT
1 TTGCAAAACTGAGAAGATAATAAGAACAAGAAAACACATAGATAC
17149617 TTGCAAAACTGAGAAGA
1 TTGCAAAACTGAGAAGA
17149634 ACATATTGGC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 17 0.31
45 36 0.65
46 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (45 bp):
TTGCAAAACTGAGAAGATAATAAGAACAAGAAAACACATAGATAC
Found at i:17153586 original size:2 final size:2
Alignment explanation
Indices: 17153579--17153614 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17153569 TACAAAACAT
17153579 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
17153615 GAACAATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17154657 original size:15 final size:15
Alignment explanation
Indices: 17154637--17154671 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17154627 ACAAAAAAAA
17154637 TTATATATGTATATT
1 TTATATATGTATATT
*
17154652 TTATATATGTATTTT
1 TTATATATGTATATT
17154667 TTATA
1 TTATA
17154672 GTCTAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
TTATATATGTATATT
Found at i:17155538 original size:20 final size:20
Alignment explanation
Indices: 17155509--17155550 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17155499 AGGGAGGAAG
17155509 AAAGAAAGAAAAGAAAAGAA
1 AAAGAAAGAAAAGAAAAGAA
* *
17155529 AAAGAGAGAAAAGAAAGGAA
1 AAAGAAAGAAAAGAAAAGAA
17155549 AA
1 AA
17155551 GTTTTCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAAGAAAAGAA
Found at i:17159853 original size:45 final size:45
Alignment explanation
Indices: 17159788--17159961 Score: 188
Period size: 45 Copynumber: 3.9 Consensus size: 45
17159778 TACGCCTAAA
* *
17159788 ATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGATATAG
1 ATGAGAAAGACCATAGCTGAAAGATGCTATGACATCATGATATAG
* * * ** *
17159833 ATGAGAAAGACCATAACTGAAAGATGTTATGGCATCACCATAAAG
1 ATGAGAAAGACCATAGCTGAAAGATGCTATGACATCATGATATAG
* * * *
17159878 ATGAGTAAA-ACCATAGCCGAAAGACGCTATGGCATCATGATATAA
1 ATGAG-AAAGACCATAGCTGAAAGATGCTATGACATCATGATATAG
* * * *
17159923 ATAAGTAAGACCATGGCTGAAAGATACTATGACATCATG
1 ATGAGAAAGACCATAGCTGAAAGATGCTATGACATCATG
17159962 GTAACAAGAC
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 2 0.02
45 101 0.95
46 3 0.03
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (45 bp):
ATGAGAAAGACCATAGCTGAAAGATGCTATGACATCATGATATAG
Found at i:17159943 original size:90 final size:89
Alignment explanation
Indices: 17159784--17159947 Score: 229
Period size: 90 Copynumber: 1.8 Consensus size: 89
17159774 GCTATACGCC
* * * * * *
17159784 TAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGATATAGATGAGAAAGACCATAA
1 TAAAATGAGTAAAACCATAGCCGAAAGACGCTATGACATCATGATATAAATAAGAAAGACCATAA
17159849 CTGAAAGATGTTATGGCATCACCA
66 CTGAAAGATGTTATGGCATCACCA
* * *
17159873 TAAAGATGAGTAAAACCATAGCCGAAAGACGCTATGGCATCATGATATAAATAAGTAAGACCATG
1 TAAA-ATGAGTAAAACCATAGCCGAAAGACGCTATGACATCATGATATAAATAAGAAAGACCATA
*
17159938 GCTGAAAGAT
65 ACTGAAAGAT
17159948 ACTATGACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
89 4 0.06
90 60 0.94
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (89 bp):
TAAAATGAGTAAAACCATAGCCGAAAGACGCTATGACATCATGATATAAATAAGAAAGACCATAA
CTGAAAGATGTTATGGCATCACCA
Found at i:17161020 original size:34 final size:34
Alignment explanation
Indices: 17160977--17161044 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
17160967 ACGATGAAAG
* *
17160977 GGTTATATACTCGCCAATAAACAAGAATTCACAT
1 GGTTATATACCCGCAAATAAACAAGAATTCACAT
* *
17161011 GGTTATATACCCTCAAATAAATAAGAATTCACAT
1 GGTTATATACCCGCAAATAAACAAGAATTCACAT
17161045 TCGTCAAGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (34 bp):
GGTTATATACCCGCAAATAAACAAGAATTCACAT
Found at i:17162383 original size:45 final size:44
Alignment explanation
Indices: 17162241--17162461 Score: 199
Period size: 45 Copynumber: 4.9 Consensus size: 44
17162231 GGCTATACGC
* * * *
17162241 ATAAAATGAGTAAGAACATAGCTAAAAGATTCTATGGCATCATG
1 ATAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATG
* * * * * **
17162285 ATAAAGATAAGTAAGACCGTAACTAAAAGATGTTATGACATCACC
1 ATAAA-ATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATG
* * * *
17162330 ATAAAAATGAGTAAAACCATAGTTGAAAGACGCTATGGCATCATG
1 AT-AAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATG
* * * *
17162375 ATATAAATGAATAAGACCATGGTTGAAAGATGCTATGACATTATG
1 ATA-AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATG
* * **
17162420 GTAAACATGACTAAGACCATAGCTGAAAGACACTATGACATC
1 ATAAA-ATGAGTAAGACCATAGCTGAAAGATGCTATGACATC
17162462 CTAGTAGTCT
Statistics
Matches: 140, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
44 8 0.06
45 129 0.92
46 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (44 bp):
ATAAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATG
Found at i:17162404 original size:90 final size:90
Alignment explanation
Indices: 17162243--17162461 Score: 219
Period size: 90 Copynumber: 2.4 Consensus size: 90
17162233 CTATACGCAT
* ** *
17162243 AAAATGAGTAAGAA-CATAGCTAAAAGATTCTATGGCATCATGATAAAGATAAGTAAGACCGTAA
1 AAAATGAGTAA-AACCATAGCTGAAAGACACTATGGCATCATGATAAAGATAAGTAAGACCATAA
*
17162307 CTAAAAGATGTTATGACATCACCATA
65 CTAAAAGATGCTATGACATCACCATA
* * *
17162333 AAAATGAGTAAAACCATAGTTGAAAGACGCTATGGCATCATGATATAA-ATGAA-TAAGACCATG
1 AAAATGAGTAAAACCATAGCTGAAAGACACTATGGCATCATGATA-AAGAT-AAGTAAGACCATA
** * * ***
17162396 GTTGAAAGATGCTATGACATTATGGTA
64 ACTAAAAGATGCTATGACATCACCATA
* * * *
17162423 AACATGACTAAGACCATAGCTGAAAGACACTATGACATC
1 AAAATGAGTAAAACCATAGCTGAAAGACACTATGGCATC
17162462 CTAGTAGTCT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
89 2 0.02
90 100 0.94
91 4 0.04
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.23
Consensus pattern (90 bp):
AAAATGAGTAAAACCATAGCTGAAAGACACTATGGCATCATGATAAAGATAAGTAAGACCATAAC
TAAAAGATGCTATGACATCACCATA
Found at i:17162555 original size:16 final size:16
Alignment explanation
Indices: 17162534--17162565 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17162524 ATCGTGTAAG
17162534 ACCATAGTTGAAAGAT
1 ACCATAGTTGAAAGAT
17162550 ACCATAGTTGAAAGAT
1 ACCATAGTTGAAAGAT
17162566 GCTATGGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
ACCATAGTTGAAAGAT
Found at i:17167215 original size:38 final size:37
Alignment explanation
Indices: 17167170--17167268 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 37
17167160 GAAATCCTTG
* *
17167170 TTATAATTATTGTAATTATAATTTAGGATCGAATATTA
1 TTATAATTATTGTAATTATAATTTAGG-TCAAACATTA
* * * **
17167208 TTATAATTACTATAATTGTAATTTTTTGTCAAACATTA
1 TTATAATTATTGTAATTATAA-TTTAGGTCAAACATTA
*
17167246 TTATAATTATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
17167269 ATTATATTCG
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
37 2 0.04
38 43 0.88
39 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (37 bp):
TTATAATTATTGTAATTATAATTTAGGTCAAACATTA
Found at i:17176330 original size:45 final size:45
Alignment explanation
Indices: 17176266--17176352 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
17176256 CAGATACTCG
* *
17176266 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
*
17176311 GTGGAATCAGCACATAGCAACCACTTTACTAATCAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
17176353 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:17176421 original size:51 final size:50
Alignment explanation
Indices: 17176352--17176549 Score: 229
Period size: 51 Copynumber: 3.9 Consensus size: 50
17176342 ATCAATGATG
* * *
17176352 TTCGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCA
* * * * *
17176403 TTCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCA
* * * * *
17176454 -TCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGAGC-TATCA
1 TTC-GGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA
17176503 TTCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 TT-CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
17176550 CACTTTCACT
Statistics
Matches: 120, Mismatches: 22, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 2 0.02
50 40 0.33
51 76 0.63
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA
Found at i:17176537 original size:101 final size:101
Alignment explanation
Indices: 17176361--17176545 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
17176351 GTTCGGTTCA
*
17176361 CATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGCCTGCA
17176426 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
* * * *
17176463 CATAGTAGCCTGCACATAGTACTACACATGCGAGC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATT-CGATACACGTAGTAGCCTGCA
*
17176527 CATAGTACTACACATGTGA
65 CATAGTACTACACACGTGA
17176546 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 6 0.08
101 38 0.50
102 32 0.42
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTGGTACG
Found at i:17176568 original size:101 final size:101
Alignment explanation
Indices: 17176356--17176579 Score: 272
Period size: 101 Copynumber: 2.2 Consensus size: 101
17176346 ATGATGTTCG
*
17176356 GTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCGATACACGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGC
* **
17176421 CTGCACATAGTACTACACACGTGATCGAAACTATCTG
65 CTGCACATAGTACTACACACGTGATCCAAACTATCAC
* * * * * *
17176458 GTACGCATAGTAGCCTGCACATAGTACTACACATGCGAGC-TATCATTCCGGTACACGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACCATT-CGATACACGTAGTAGC
* * *
17176522 CTGCACATAGTACTACACATGTGA-CCATCACTTTCAC
65 CTGCACATAGTACTACACACGTGATCCA-AACTATCAC
* *
17176559 TTTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTACACA
17176580 CAATCCATGC
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
100 8 0.08
101 59 0.58
102 35 0.34
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCC
TGCACATAGTACTACACACGTGATCCAAACTATCAC
Found at i:17182727 original size:22 final size:21
Alignment explanation
Indices: 17182696--17182754 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
17182686 CAGTTTTTTT
*
17182696 TTTTTATATTTTAAGTTTTT-A
1 TTTTAATATTTTAA-TTTTTAA
*
17182717 TTTTAATTATTGTAATTTTTGAA
1 TTTTAA-TATTTTAATTTTT-AA
*
17182740 TTTTAAAATTTTAAT
1 TTTTAATATTTTAAT
17182755 CTCGATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 10 0.32
22 14 0.45
23 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTAATATTTTAATTTTTAA
Found at i:17187477 original size:19 final size:19
Alignment explanation
Indices: 17187453--17187489 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17187443 TATGCTGCAC
17187453 TATAAATAAT-TATTTATAA
1 TATAAA-AATATATTTATAA
17187472 TATAAAAATATATTTATA
1 TATAAAAATATATTTATA
17187490 TATTTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAAAATATATTTATAA
Found at i:17187543 original size:31 final size:31
Alignment explanation
Indices: 17187507--17187569 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
17187497 CTTTGAAATG
* * *
17187507 TATACA-ATTAAATCAAAATTAAAGTTTCATA
1 TATACATA-TAAACCAAAATAAAAATTTCATA
*
17187538 TATACATATAAACCACAATAAAAATTTCATA
1 TATACATATAAACCAAAATAAAAATTTCATA
17187569 T
1 T
17187570 TTATAGTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (31 bp):
TATACATATAAACCAAAATAAAAATTTCATA
Found at i:17198228 original size:18 final size:18
Alignment explanation
Indices: 17198201--17198243 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
17198191 CGCATAAAAA
* *
17198201 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
17198219 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
17198237 GAAAGAA
1 GAAAGAA
17198244 GGGGGGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:17199893 original size:14 final size:14
Alignment explanation
Indices: 17199874--17199900 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17199864 TAAGTAAGCT
17199874 CTCCCTCCCTCTCC
1 CTCCCTCCCTCTCC
17199888 CTCCCTCCCTCTC
1 CTCCCTCCCTCTC
17199901 TCCAACCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (14 bp):
CTCCCTCCCTCTCC
Found at i:17209311 original size:15 final size:16
Alignment explanation
Indices: 17209282--17209311 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17209272 CAAACATGCT
17209282 TTAACACATTATCAAA
1 TTAACACATTATCAAA
17209298 TTAACACA-TATCAA
1 TTAACACATTATCAA
17209312 CATGGCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:17216435 original size:24 final size:24
Alignment explanation
Indices: 17216406--17216491 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
17216396 TACTACAAAA
* *
17216406 CACTTATAGAATACG-TAACAAAGG
1 CACTTACAGAATACGCCAA-AAAGG
*
17216430 TACTTACAGAATACGCCAAAAAGG
1 CACTTACAGAATACGCCAAAAAGG
* *
17216454 CACTTACAGAATACCCCACAAAGG
1 CACTTACAGAATACGCCAAAAAGG
*
17216478 CACTTACGGAATAC
1 CACTTACAGAATAC
17216492 CCTGCTTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 52 0.96
25 2 0.04
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.17
Consensus pattern (24 bp):
CACTTACAGAATACGCCAAAAAGG
Found at i:17216492 original size:24 final size:24
Alignment explanation
Indices: 17216423--17216493 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
17216413 AGAATACGTA
* *
17216423 ACAAAGGTACTTACAGAATACGCC
1 ACAAAGGCACTTACAGAATACCCC
*
17216447 AAAAAGGCACTTACAGAATACCCC
1 ACAAAGGCACTTACAGAATACCCC
*
17216471 ACAAAGGCACTTACGGAATACCC
1 ACAAAGGCACTTACAGAATACCC
17216494 TGCTTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.14
Consensus pattern (24 bp):
ACAAAGGCACTTACAGAATACCCC
Found at i:17219037 original size:29 final size:30
Alignment explanation
Indices: 17219002--17219065 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
17218992 GGGATTTGGT
**
17219002 GATTTTATTTCACTTATTCATTATTTAGC-
1 GATTTTATCACACTTATTCATTATTTAGCA
* * *
17219031 GATTTTATCACATTTATTCGTTATTTGGCA
1 GATTTTATCACACTTATTCATTATTTAGCA
17219061 GATTT
1 GATTT
17219066 CAGCAGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.53
Consensus pattern (30 bp):
GATTTTATCACACTTATTCATTATTTAGCA
Found at i:17227235 original size:12 final size:12
Alignment explanation
Indices: 17227218--17227244 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17227208 TTTGATTAAG
17227218 TATTTATTACTT
1 TATTTATTACTT
17227230 TATTTATTACTT
1 TATTTATTACTT
17227242 TAT
1 TAT
17227245 ATATCACAAC
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:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTATTACTT
Found at i:17227470 original size:19 final size:18
Alignment explanation
Indices: 17227443--17227481 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17227433 ATTGCGTGTT
* *
17227443 TGAATAGAAATAAACGAAA
1 TGAAAAGAAA-AAAAGAAA
17227462 TGAAAAGAAAAAAAGAAA
1 TGAAAAGAAAAAAAGAAA
17227480 TG
1 TG
17227482 GGAAACATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.13
Consensus pattern (18 bp):
TGAAAAGAAAAAAAGAAA
Found at i:17229494 original size:2 final size:2
Alignment explanation
Indices: 17229487--17229520 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17229477 ATGTATTCGA
17229487 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
17229521 TAAGCTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17230599 original size:41 final size:41
Alignment explanation
Indices: 17230554--17230656 Score: 179
Period size: 41 Copynumber: 2.5 Consensus size: 41
17230544 TGATCTAGTA
*
17230554 CACCGACATTAAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
*
17230595 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
*
17230636 CACCGGCATTAAGCCTACTAG
1 CACCGGCATTAAGCCTGCTAG
17230657 GCACAAGCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:17231087 original size:2 final size:2
Alignment explanation
Indices: 17231080--17231104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17231070 TGTCTATGTG
17231080 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 T
17231105 TCTACTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17232220 original size:18 final size:18
Alignment explanation
Indices: 17232197--17232237 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
17232187 TATTTACACG
17232197 ATTAAACCATTTTCTCAA
1 ATTAAACCATTTTCTCAA
17232215 ATTAAACCATTTTCTCAA
1 ATTAAACCATTTTCTCAA
17232233 ATTAA
1 ATTAA
17232238 GCACTCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAAACCATTTTCTCAA
Found at i:17241849 original size:16 final size:15
Alignment explanation
Indices: 17241821--17241858 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
17241811 TAAATAATTA
17241821 AATTTTA-TTGAAACT
1 AATTTTATTTGAAA-T
17241836 AATTTTATTTGAAAT
1 AATTTTATTTGAAAT
*
17241851 AATATTAT
1 AATTTTAT
17241859 GTATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (15 bp):
AATTTTATTTGAAAT
Found at i:17242946 original size:37 final size:37
Alignment explanation
Indices: 17242868--17242951 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
17242858 GAAACATCTT
* ** *
17242868 GTTTCGATACTAAACTAAAATAATAAGTCTAGTTTCT
1 GTTTCGATATTAAACTAAAATAATAAGTCTAAATTCC
*
17242905 GTTTCAATATTAAACTAAAATAATAAGTCTAAATTCC
1 GTTTCGATATTAAACTAAAATAATAAGTCTAAATTCC
17242942 GTTTCGATAT
1 GTTTCGATAT
17242952 AAATTTCAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (37 bp):
GTTTCGATATTAAACTAAAATAATAAGTCTAAATTCC
Found at i:17243164 original size:24 final size:24
Alignment explanation
Indices: 17243137--17243186 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
17243127 ATATATATAT
* * **
17243137 ATATATATATATTAAATCTATTTA
1 ATATATAAATATAAAATAAATTTA
17243161 ATATATAAATATAAAATAAATTTA
1 ATATATAAATATAAAATAAATTTA
17243185 AT
1 AT
17243187 TAGCGTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATAAATATAAAATAAATTTA
Found at i:17243167 original size:2 final size:2
Alignment explanation
Indices: 17243117--17243148 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17243107 ATACCTTCCA
17243117 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
17243149 TAAATCTATT
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):
AT
Found at i:17243962 original size:17 final size:18
Alignment explanation
Indices: 17243936--17243969 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17243926 TTGTTTATAA
17243936 TTTAAAAAA-TTAATTAT
1 TTTAAAAAATTTAATTAT
*
17243953 TTTAAGAAATTTAATTA
1 TTTAAAAAATTTAATTA
17243970 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTAAAAAATTTAATTAT
Found at i:17243968 original size:18 final size:17
Alignment explanation
Indices: 17243936--17243969 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17243926 TTGTTTATAA
17243936 TTTAAAAAATTAATTAT
1 TTTAAAAAATTAATTAT
*
17243953 TTTAAGAAATTTAATTA
1 TTTAA-AAAATTAATTA
17243970 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAAAAATTAATTAT
Found at i:17246235 original size:2 final size:2
Alignment explanation
Indices: 17246228--17246281 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
17246218 ACAGTAAATA
17246228 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17246270 AG AG AG AG AG AG
1 AG AG AG AG AG AG
17246282 TGATGGGTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17249609 original size:22 final size:22
Alignment explanation
Indices: 17249550--17249609 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
17249540 AAACAATTAA
* *
17249550 AATTTCAATTAAACA-GCATTAC
1 AATTT-AATTAAAAATGCATAAC
**
17249572 AATTATAATTCCAAATGCATAAC
1 AATT-TAATTAAAAATGCATAAC
17249595 AATTTAATTAAAAAT
1 AATTTAATTAAAAAT
17249610 CTGCATGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (22 bp):
AATTTAATTAAAAATGCATAAC
Found at i:17252913 original size:30 final size:30
Alignment explanation
Indices: 17252873--17252940 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
17252863 TTAAAGGATC
* *
17252873 TGAAAATGCAAATGTG-ATTGATTACAGGGTA
1 TGAATATGCAAATGTGAATGGA--ACAGGGTA
17252904 TG-ATATGCAAATGTGAATGGAACAGGGTA
1 TGAATATGCAAATGTGAATGGAACAGGGTA
17252933 TGAATATG
1 TGAATATG
17252941 TTAATATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 10 0.30
30 17 0.52
31 6 0.18
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAATATGCAAATGTGAATGGAACAGGGTA
Found at i:17257865 original size:24 final size:24
Alignment explanation
Indices: 17257832--17257877 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17257822 ATTGATATAA
* **
17257832 TGGTATCCTTTTTGACCTTTTCAT
1 TGGTAACCTTTTCCACCTTTTCAT
17257856 TGGTAACCTTTTCCACCTTTTC
1 TGGTAACCTTTTCCACCTTTTC
17257878 TTTGTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.11, T:0.50
Consensus pattern (24 bp):
TGGTAACCTTTTCCACCTTTTCAT
Found at i:17258774 original size:13 final size:13
Alignment explanation
Indices: 17258754--17258785 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17258744 TTGACTCATA
17258754 AATATTAATTAAT
1 AATATTAATTAAT
*
17258767 AGTATTAATTAAT
1 AATATTAATTAAT
17258780 AATATT
1 AATATT
17258786 TATGAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AATATTAATTAAT
Found at i:17263278 original size:36 final size:36
Alignment explanation
Indices: 17263226--17263302 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
17263216 TAATTTAACC
*
17263226 TTAATCATGCTTAGTGGATGTTGCCATCACTATCTA
1 TTAACCATGCTTAGTGGATGTTGCCATCACTATCTA
17263262 TTAACCATGCTTAGTGGATGTTGCCATCACTATCTA
1 TTAACCATGCTTAGTGGATGTTGCCATCACTATCTA
17263298 TTAAC
1 TTAAC
17263303 TTCACATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (36 bp):
TTAACCATGCTTAGTGGATGTTGCCATCACTATCTA
Found at i:17267555 original size:13 final size:13
Alignment explanation
Indices: 17267537--17267562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17267527 AAAATTTGAT
17267537 AGATGATAAATAA
1 AGATGATAAATAA
17267550 AGATGATAAATAA
1 AGATGATAAATAA
17267563 TAAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AGATGATAAATAA
Found at i:17268630 original size:27 final size:25
Alignment explanation
Indices: 17268581--17268653 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
17268571 CCCGATATAT
* * **
17268581 GGCTCTTTAGAGCTGCCCAATTAAA
1 GGCTCTTTGGAGCTTCCTGATTAAA
*
17268606 GGCTCTTTTGTGAGCTTCCTGATTAAT
1 GGCTC-TTTG-GAGCTTCCTGATTAAA
*
17268633 GGCTCTTTGGAGCTTCTTGAT
1 GGCTCTTTGGAGCTTCCTGAT
17268654 ATTGGCTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 16 0.40
26 7 0.17
27 17 0.43
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCTGATTAAA
Found at i:17268653 original size:25 final size:27
Alignment explanation
Indices: 17268600--17268661 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
17268590 GAGCTGCCCA
*
17268600 ATTAAAGGCTCTTTTGTGAGCTTCCTG
1 ATTAATGGCTCTTTTGTGAGCTTCCTG
*
17268627 ATTAATGGCTC-TTTG-GAGCTTCTTG
1 ATTAATGGCTCTTTTGTGAGCTTCCTG
*
17268652 A-TATTGGCTC
1 ATTAATGGCTC
17268662 GTTTAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.25
25 10 0.31
26 4 0.12
27 10 0.31
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (27 bp):
ATTAATGGCTCTTTTGTGAGCTTCCTG
Done.