Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 81 of 120
Found at i:24334536 original size:23 final size:23
Alignment explanation
Indices: 24334507--24334809 Score: 282
Period size: 23 Copynumber: 12.7 Consensus size: 23
24334497 TTTGATGTAA
*
24334507 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
*** *
24334530 CCTAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
24334553 TAAAAACCCTAACATTAACCTAATTTAAT
1 TAAAAA-CC---C--TAACCTAATTTAAT
24334582 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
24334611 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
24334634 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
**
24334657 TAAAAACCCTAGTCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
24334680 TAAAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
24334704 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
24334730 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
24334753 TAAAAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
24334775 T-----CCCTAAACCCTAATTTAAT
1 TAAAAACCCT-AA-CCTAATTTAAT
24334795 TAAAAACCCTAACCT
1 TAAAAACCCTAACCT
24334810 TAACGTAATG
Statistics
Matches: 237, Mismatches: 15, Indels: 56
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.02
18 2 0.01
19 10 0.04
20 1 0.00
22 1 0.00
23 135 0.57
24 10 0.04
25 15 0.06
26 5 0.02
27 10 0.04
29 40 0.17
30 3 0.01
33 1 0.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:24334575 original size:29 final size:29
Alignment explanation
Indices: 24334539--24334667 Score: 156
Period size: 29 Copynumber: 4.9 Consensus size: 29
24334529 CCCTAAACCC
*
24334539 TAACCTAAATTAATTAAAAACCCTAACAT
1 TAACCTAATTTAATTAAAAACCCTAACAT
*
24334568 TAACCTAATTTAATTAAAAACCCTAACCT
1 TAACCTAATTTAATTAAAAACCCTAACAT
24334597 TAACCTAATTTAATTAAAAA-CC---C--
1 TAACCTAATTTAATTAAAAACCCTAACAT
24334620 TAACCTAATTTAATTAAAAA-CC---C--
1 TAACCTAATTTAATTAAAAACCCTAACAT
24334643 TAACCTAATTTAATTAAAAACCCTA
1 TAACCTAATTTAATTAAAAACCCTA
24334668 GTCTAATTTA
Statistics
Matches: 95, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
23 43 0.45
24 2 0.02
25 1 0.01
28 2 0.02
29 47 0.49
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (29 bp):
TAACCTAATTTAATTAAAAACCCTAACAT
Found at i:24334737 original size:96 final size:94
Alignment explanation
Indices: 24334615--24334818 Score: 302
Period size: 96 Copynumber: 2.1 Consensus size: 94
24334605 TTTAATTAAA
* **
24334615 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGTCTAATTTAAT
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
*
24334680 -TAAAAACCCTAAACCCTTAATTAAAAACCCT
66 CCAAAAACCCT-AA--CTTAATTAAAAACCCT
24334711 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
** *
24334776 CCCTAAACCCTAATTTAATTAAAAACCCT
66 CCAAAAACCCTAACTTAATTAAAAACCCT
*
24334805 AACCTTAACGTAAT
1 AACCTTAACCTAAT
24334819 GTTAGATTTG
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 28 0.28
96 64 0.65
97 7 0.07
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (94 bp):
AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
CCAAAAACCCTAACTTAATTAAAAACCCT
Found at i:24334948 original size:115 final size:116
Alignment explanation
Indices: 24334815--24335031 Score: 366
Period size: 116 Copynumber: 1.9 Consensus size: 116
24334805 AACCTTAACG
*
24334815 TAATGTTAGATTTGGAAAAATG-TTTGACTGGTACTAACAAA-TAATAATTTTACATAATTTGAT
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAA-AAATTAATAATTGTACATAATTTGAT
* *
24334878 AATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
65 AATTTTACTAACCATTAATACAATTTTTTAACGTAATAATTTTACATTCACA
*
24334930 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAAAAATTAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAAAAATTAATAATTGTACATAATTTGATA
*
24334995 ATTTTCCTAACCATTAATACAATTTTTTAACGTAATA
66 ATTTTACTAACCATTAATACAATTTTTTAACGTAATA
24335032 CAATTTATCA
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
115 25 0.26
116 70 0.74
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAAAAATTAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTAACGTAATAATTTTACATTCACA
Found at i:24338282 original size:125 final size:126
Alignment explanation
Indices: 24338060--24338412 Score: 530
Period size: 126 Copynumber: 2.8 Consensus size: 126
24338050 CCCAAACATG
* * * *
24338060 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGAGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
24338125 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-ATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * * *
24338185 CTACTGTAGCAAAAGAGCG-CTGACGATGCCGCGATTTCACAAATTTTTCTCAACTAGCATCCTG
1 CTACTGTAGCAAAAGAGCGTC-CACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
24338249 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * * *
24338311 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGAGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
24338376 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
24338413 CTCGAAATTA
Statistics
Matches: 204, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
124 1 0.00
125 96 0.47
126 106 0.52
127 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGAGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
Found at i:24338362 original size:126 final size:125
Alignment explanation
Indices: 24338060--24338438 Score: 553
Period size: 125 Copynumber: 3.0 Consensus size: 125
24338050 CCCAAACATG
* *
24338060 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
24338125 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
* * * * * *
24338185 CTACTGTAGCAAAAGAGCG-CTGACGATGCCGCGATTTCACAAATTTTTCTCAACTAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
24338249 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCATGAC
* *
24338311 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** **** *
24338376 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
24338436 CTA
1 CTA
24338439 AAAACCCTTA
Statistics
Matches: 225, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.00
125 116 0.52
126 107 0.48
127 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
Found at i:24340121 original size:26 final size:26
Alignment explanation
Indices: 24340060--24340121 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 26
24340050 ATGCTTTGGG
* *
24340060 ATTAATAAGATTATTATTAAATATATT
1 ATTAATAA-AATACTATTAAATATATT
24340087 -TTAAT--AATACTATT-AATATATTT
1 ATTAATAAAATACTATTAAATATA-TT
24340110 ATTAATAAAATA
1 ATTAATAAAATA
24340122 TGAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 6 0.21
23 9 0.31
24 5 0.17
26 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTAATAAAATACTATTAAATATATT
Found at i:24346071 original size:2 final size:2
Alignment explanation
Indices: 24346064--24346100 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24346054 GATAGATTGT
24346064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24346101 CCATATGGTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24352984 original size:25 final size:26
Alignment explanation
Indices: 24352946--24352997 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
24352936 AGTTGTAAAT
24352946 TGGAAAAATATCTTCAG-AAATTTTC
1 TGGAAAAATATCTTCAGAAAATTTTC
* * *
24352971 TGGAACAATCTCTTTAGAAAATTTTC
1 TGGAAAAATATCTTCAGAAAATTTTC
24352997 T
1 T
24352998 CTCTATAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (26 bp):
TGGAAAAATATCTTCAGAAAATTTTC
Found at i:24355810 original size:20 final size:21
Alignment explanation
Indices: 24355765--24355817 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
24355755 ATGTCAAATA
*
24355765 TATTTTTATTTATGAAAAGTG
1 TATTTTTATTTATAAAAAGTG
*
24355786 AATTTTT-TTTATAAAAGAGT-
1 TATTTTTATTTATAAAA-AGTG
*
24355806 TATTTTGATTTA
1 TATTTTTATTTA
24355818 ACAATCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (21 bp):
TATTTTTATTTATAAAAAGTG
Found at i:24368123 original size:19 final size:19
Alignment explanation
Indices: 24368096--24368136 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
24368086 TGATTTATTT
*
24368096 TAAGCTTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
24368115 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
24368134 TAA
1 TAA
24368137 CTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:24368888 original size:17 final size:17
Alignment explanation
Indices: 24368848--24368889 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
24368838 ATATGCAAAC
*
24368848 AAAAACCTCGACTCATA
1 AAAAACTTCGACTCATA
24368865 AAAAACTTCGACTCATA
1 AAAAACTTCGACTCATA
24368882 AAAAACTT
1 AAAAACTT
24368890 GTTAAGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAACTTCGACTCATA
Found at i:24370618 original size:20 final size:20
Alignment explanation
Indices: 24370593--24370632 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24370583 TATTCAAACA
* *
24370593 ATATTACTTGAATAGTTATG
1 ATATTACATGAATAATTATG
*
24370613 ATATTAGATGAATAATTATG
1 ATATTACATGAATAATTATG
24370633 CCTATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATG
Found at i:24370711 original size:22 final size:24
Alignment explanation
Indices: 24370672--24370720 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
24370662 AGACACCTAT
*
24370672 TGAAAATGTCTCTATAAAGAGACA
1 TGAAAATGTCTCTATAAAGAGAAA
*
24370696 TGAAAAT-TC-CTATAAATAGAAA
1 TGAAAATGTCTCTATAAAGAGAAA
24370718 TGA
1 TGA
24370721 GATTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 2 0.09
24 7 0.30
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
TGAAAATGTCTCTATAAAGAGAAA
Found at i:24373014 original size:12 final size:11
Alignment explanation
Indices: 24372997--24373032 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
24372987 AACAAATCCT
24372997 CTCTCATATTTC
1 CTCTCA-ATTTC
*
24373009 CTCTCAATTTT
1 CTCTCAATTTC
24373020 CTCTCAATTTC
1 CTCTCAATTTC
24373031 CT
1 CT
24373033 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:24373043 original size:22 final size:23
Alignment explanation
Indices: 24372996--24373044 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
24372986 AAACAAATCC
**
24372996 TCTCTCATATTTCCTCTCAATTT
1 TCTCTCATATTTCCTCTCAAAAT
24373019 TCTCTCA-ATTTCCT-TCCAAAAT
1 TCTCTCATATTTCCTCT-CAAAAT
24373041 TCTC
1 TCTC
24373045 ATAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTCTCATATTTCCTCTCAAAAT
Found at i:24373077 original size:51 final size:51
Alignment explanation
Indices: 24373012--24373134 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
24373002 ATATTTCCTC
* * *
24373012 TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTC-TCAAACCCATATTTAATT
* * *
24373063 TCAATTTCCTCTCAAATTCATTCTAAAAATCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
*
24373114 TCAATTTGCTCTCAATTTCCT
1 TCAATTTCCTCTCAATTTCCT
24373135 GTTTTAAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.31, C:0.25, G:0.01, T:0.43
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
Found at i:24375378 original size:25 final size:25
Alignment explanation
Indices: 24375349--24375462 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
24375339 TTTAAATTTG
24375349 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
24375374 TTATTTGATGTAATACACATAGAAAGT
1 TTATTTGATGTAATA-AAATAG-AAGT
* ** *
24375401 TT-TTCGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
24375419 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
24375445 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
24375463 ACCCTAACCT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 4 0.06
21 4 0.06
23 2 0.03
24 3 0.04
25 35 0.51
26 10 0.15
27 6 0.09
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:24375545 original size:29 final size:29
Alignment explanation
Indices: 24375462--24375789 Score: 484
Period size: 29 Copynumber: 11.4 Consensus size: 29
24375452 ATGTAATAAA
* ** *
24375462 AACCCTAACCTAATTTAGTTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * * *
24375491 AA-CCT-A-A-ACCCCAATTAAGAATCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
24375516 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
24375545 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
24375574 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
24375603 AACCCTAACATAACTTAATTAAAAGCCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
24375632 AACCCTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
24375661 AACCCTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
24375690 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
24375719 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
24375748 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
24375777 AACCCTAACATAA
1 AACCCTAACATAA
24375790 TAATTTTACA
Statistics
Matches: 274, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
25 13 0.05
26 3 0.01
27 2 0.01
28 3 0.01
29 253 0.92
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (29 bp):
AACCCTAACATAACCTAATTAAAAACCCT
Found at i:24375847 original size:55 final size:55
Alignment explanation
Indices: 24375787--24375963 Score: 336
Period size: 55 Copynumber: 3.2 Consensus size: 55
24375777 AACCCTAACA
24375787 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
24375842 TAATAATTTTACATAATTGGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
24375897 TAATAATTTTACATAAATTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
24375952 TAATAATTTTAC
1 TAATAATTTTAC
24375964 TAACAATTAA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 119 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.43
Consensus pattern (55 bp):
TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
Found at i:24375958 original size:92 final size:92
Alignment explanation
Indices: 24375862--24376035 Score: 330
Period size: 92 Copynumber: 1.9 Consensus size: 92
24375852 ACATAATTGG
24375862 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAAATTGATAATTTTAC
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAAATTGATAATTTTAC
24375927 TAACAATTAACACAATTTTTGGACTTA
66 TAACAATTAACACAATTTTTGGACTTA
*
24375954 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTAC
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAAATTGATAATTTTAC
*
24376019 TAACAATTAATACAATT
66 TAACAATTAACACAATT
24376036 ATCAATTAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 80 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (92 bp):
ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAAATTGATAATTTTAC
TAACAATTAACACAATTTTTGGACTTA
Found at i:24375959 original size:37 final size:37
Alignment explanation
Indices: 24375917--24376000 Score: 168
Period size: 37 Copynumber: 2.3 Consensus size: 37
24375907 ACATAAATTG
24375917 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
24375954 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
24375991 ATAATTTTAC
1 ATAATTTTAC
24376001 ATAATTTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (37 bp):
ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
Found at i:24376083 original size:147 final size:147
Alignment explanation
Indices: 24375807--24376066 Score: 422
Period size: 147 Copynumber: 1.8 Consensus size: 147
24375797 ACATAATTTG
24375807 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAATTGGATAATTTTAC
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAATTGGATAATTTTAC
* * * * *
24375872 TAACAATTAACACAATTTTTGGACTTAATAATTTTACATAAATTGATAATTTTACTAACAATTAA
66 TAACAATTAACACAATTTATGCAATTAATAATTTGACATAAAATGATAATTTTACTAACAATTAA
24375937 CACAATTTTTGGACTTA
131 CACAATTTTTGGACTTA
*
24375954 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTAC
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAATTGGATAATTTTAC
*
24376019 TAACAATTAATACAA-TTAT-CAATTAATAA-TTGA-ATAAAAT-ATAATTTT
66 TAACAATTAACACAATTTATGCAATTAATAATTTGACATAAAATGATAATTTT
24376067 TTCTAAAATT
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
142 8 0.08
143 6 0.06
144 3 0.03
145 8 0.08
146 3 0.03
147 78 0.74
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (147 bp):
ATAATTTTACTAACAATTAACACAATTTTTGGACTTAATAATTTTACATAATTGGATAATTTTAC
TAACAATTAACACAATTTATGCAATTAATAATTTGACATAAAATGATAATTTTACTAACAATTAA
CACAATTTTTGGACTTA
Found at i:24379282 original size:124 final size:125
Alignment explanation
Indices: 24379062--24379411 Score: 607
Period size: 124 Copynumber: 2.8 Consensus size: 125
24379052 CCCAAACTTG
24379062 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
24379127 TAGAAGCGATTTTATACTTTTTGCTCAGAAACGTCAAAAAAAAA-TATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
*
24379186 CTACTGTAGCAAAATAGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
24379251 TAGAAGCGATTTTATACAATTTGCTTAGAAACGT-AAAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * *
24379310 CTACTGTGGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
24379375 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
24379412 CTCGAAATAA
Statistics
Matches: 213, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
123 9 0.04
124 201 0.94
125 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:24389635 original size:42 final size:42
Alignment explanation
Indices: 24389589--24389719 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
24389579 GCCTGAAGGC
* * *
24389589 TGAACAGAAGCTCATGAGAGCTAAATGGAAACCTATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
* ** * *
24389631 TGAACGGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
* * * * *
24389673 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
24389715 TGAAC
1 TGAAC
24389720 GAAAACTCAT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
Found at i:24389725 original size:21 final size:21
Alignment explanation
Indices: 24389652--24389730 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
24389642 TTGTAAGAGC
24389652 TGAACGAAAACCCATAAGGGT
1 TGAACGAAAACCCATAAGGGT
* * * * *
24389673 TTAACTG-AAGCTCAAAAGAGT
1 TGAAC-GAAAACCCATAAGGGT
* * *
24389694 TGAATGGAAACCCATTAGGGT
1 TGAACGAAAACCCATAAGGGT
*
24389715 TGAACGAAAACTCATA
1 TGAACGAAAACCCATA
24389731 TGAGTTAACA
Statistics
Matches: 40, Mismatches: 16, Indels: 4
0.67 0.27 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
TGAACGAAAACCCATAAGGGT
Found at i:24389736 original size:42 final size:41
Alignment explanation
Indices: 24389589--24389736 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 41
24389579 GCCTGAAGGC
* * * *
24389589 TGAACAGAAGCTCATGAGAGCTAAATGGAAACCTATAAGGGT
1 TGAAC-GAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
** * * *
24389631 TGAACGGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGGGT
1 TGAAC-GAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
* * *
24389673 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAAC-GAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
* *
24389715 TGAACGAAAACTCATATGAGTT
1 TGAACG-AAGCTCATAAGAGTT
24389737 AACAGAAGCT
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
41 1 0.01
42 83 0.99
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (41 bp):
TGAACGAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
Found at i:24389881 original size:25 final size:24
Alignment explanation
Indices: 24389821--24389912 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
24389811 GGTACATTTG
24389821 CCGTCAATTCATCCTTTGCATATA
1 CCGTCAATTCATCCTTTGCATATA
* *
24389845 CCGTCAATTCATCCTTTGTATTTTA
1 CCGTCAATTCATCCTTTGCA-TATA
*
24389870 CTGTCAATTCATCCTTTGCATATA
1 CCGTCAATTCATCCTTTGCATATA
*
24389894 CCGTCAATTCATCATTTGC
1 CCGTCAATTCATCCTTTGC
24389913 CAGAGAACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 39 0.65
25 21 0.35
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (24 bp):
CCGTCAATTCATCCTTTGCATATA
Found at i:24393733 original size:13 final size:13
Alignment explanation
Indices: 24393715--24393740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24393705 TTGATTTATA
24393715 TGTGTGAAAATTT
1 TGTGTGAAAATTT
24393728 TGTGTGAAAATTT
1 TGTGTGAAAATTT
24393741 CATCGTTTGT
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:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:24394950 original size:42 final size:43
Alignment explanation
Indices: 24394897--24395008 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
24394887 TTCGATTTGA
*
24394897 GATTTACGTGTAAGACCATGTTTGGGAC-ATCGGCATCG-TATAC
1 GATTT-CGTGTAAGACCATGTCTGGGACAAT-GGCATCGATATAC
* **
24394940 GATTTCGTGTAAGACCTTGTCTGGGACAATGGCATCGATATTT
1 GATTTCGTGTAAGACCATGTCTGGGACAATGGCATCGATATAC
* * *
24394983 GATTACATGCAAGACCATGTCTGGGA
1 GATTTCGTGTAAGACCATGTCTGGGA
24395009 TGTTGGCATT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 27 0.46
43 32 0.54
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTGGGACAATGGCATCGATATAC
Found at i:24399710 original size:24 final size:24
Alignment explanation
Indices: 24399679--24399725 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
24399669 AAAGGGTAAC
* *
24399679 AAGAAGATGAAATGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
24399703 AAGAAGATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
24399726 GAACATCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:24410743 original size:24 final size:24
Alignment explanation
Indices: 24410698--24410761 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
24410688 GGGTTACAAG
* *
24410698 AAGATGAAAGGTTAAAGGTTAAAA
1 AAGATGAAAGGTGAAAGCTTAAAA
* **
24410722 AAGATGAAAGGTGGAAGCTTAAGG
1 AAGATGAAAGGTGAAAGCTTAAAA
*
24410746 GAGATGAAAGGTGAAA
1 AAGATGAAAGGTGAAA
24410762 AGTTGATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGATGAAAGGTGAAAGCTTAAAA
Found at i:24414778 original size:9 final size:9
Alignment explanation
Indices: 24414761--24414797 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
24414751 TGAGTTTTCG
24414761 AATTCGAAT
1 AATTCGAAT
*
24414770 AACTCGAAT
1 AATTCGAAT
24414779 AATTCGAAT
1 AATTCGAAT
24414788 AATTCGAAT
1 AATTCGAAT
24414797 A
1 A
24414798 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:24414993 original size:14 final size:14
Alignment explanation
Indices: 24414974--24415007 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
24414964 TTATTTTTTT
24414974 TCAAAATTTTACTC
1 TCAAAATTTTACTC
24414988 TCAAAATTTTACTC
1 TCAAAATTTTACTC
*
24415002 CCAAAA
1 TCAAAA
24415008 CCTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (14 bp):
TCAAAATTTTACTC
Found at i:24415787 original size:5 final size:5
Alignment explanation
Indices: 24415777--24415802 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
24415767 CTCAAAAATT
24415777 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
24415803 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:24416316 original size:51 final size:51
Alignment explanation
Indices: 24416240--24416342 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
24416230 TGAATTGCAT
*
24416240 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAGAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
* *
24416291 CGAGTGTAGGCTTGAGCATCACGAACCAAGTCACAAGAAAAAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
24416342 C
1 C
24416343 TTACTTTCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (51 bp):
CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
Found at i:24420660 original size:12 final size:12
Alignment explanation
Indices: 24420643--24420704 Score: 65
Period size: 12 Copynumber: 5.1 Consensus size: 12
24420633 ATATCCAAAC
*
24420643 AAAATAAAGTAA
1 AAAATAAAATAA
24420655 AAAATAATAA-AA
1 AAAATAA-AATAA
24420667 TAAAATAAAATAA
1 -AAAATAAAATAA
*
24420680 ATAATAAAAT-A
1 AAAATAAAATAA
24420691 AAAATAAAAATAA
1 AAAAT-AAAATAA
24420704 A
1 A
24420705 GAAAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
11 5 0.12
12 25 0.60
13 12 0.29
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:24420668 original size:5 final size:5
Alignment explanation
Indices: 24420643--24420715 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
24420633 ATATCCAAAC
*
24420643 AAAAT AAAGT AAAA- AATAAT AAAAT AAAAT AAAAT AAATAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT -AA-AAT AAAAT
24420690 AAAAAT AAAAAT AAAGA- AAAAT AAAA
1 -AAAAT -AAAAT AAA-AT AAAAT AAAA
24420716 CTGGGTTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 3 0.05
5 35 0.59
6 18 0.31
7 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:24420701 original size:34 final size:37
Alignment explanation
Indices: 24420645--24420714 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 37
24420635 ATCCAAACAA
*
24420645 AATAAAGTAAAAAATAATAAAATAAA-ATAAAATAAAT
1 AATAAAATAAAAAATAATAAAATAAAGA-AAAATAAAT
24420682 AATAAAAT-AAAAAT-A-AAAATAAAGAAAAATAAA
1 AATAAAATAAAAAATAATAAAATAAAGAAAAATAAA
24420715 ACTGGGTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 16 0.52
35 2 0.06
36 6 0.19
37 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (37 bp):
AATAAAATAAAAAATAATAAAATAAAGAAAAATAAAT
Found at i:24424674 original size:20 final size:17
Alignment explanation
Indices: 24424649--24424687 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
24424639 TTCTTAGAAT
24424649 TTTAATCCAATATTTTATAA
1 TTTAAT-CAAT-TTTT-TAA
24424669 TTTAATCAATTTTTTAA
1 TTTAATCAATTTTTTAA
24424686 TT
1 TT
24424688 GATTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 4 0.21
20 6 0.32
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATCAATTTTTTAA
Found at i:24429427 original size:18 final size:17
Alignment explanation
Indices: 24429388--24429447 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
24429378 ATATTATTTT
24429388 TTAATATTATTTAAATA
1 TTAATATTATTTAAATA
24429405 TTAATATTAATTT--ATA
1 TTAATATT-ATTTAAATA
*
24429421 CT-ATAATTATTTAAAATA
1 TTAAT-ATTATTT-AAATA
24429439 TTAAT-TTAT
1 TTAATATTAT
24429448 AGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 6 0.17
16 7 0.20
17 12 0.34
18 8 0.23
19 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTATTTAAATA
Found at i:24435374 original size:25 final size:25
Alignment explanation
Indices: 24435339--24435395 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
24435329 ACATAAACGC
24435339 AGCTCTTTATGAGCGTCCTGAT-AT
1 AGCTCTTTATGAGCGTCCTGATAAT
*
24435363 AGGCTCTTTATGAGCTTCCTGATAAT
1 A-GCTCTTTATGAGCGTCCTGATAAT
24435389 AGCTCTT
1 AGCTCTT
24435396 CGGAGTTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 26 0.87
26 3 0.10
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (25 bp):
AGCTCTTTATGAGCGTCCTGATAAT
Found at i:24436843 original size:12 final size:13
Alignment explanation
Indices: 24436826--24436855 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24436816 TATTTTAGTC
24436826 AACAC-AGGCAGA
1 AACACAAGGCAGA
24436838 AACACAAGGCAGA
1 AACACAAGGCAGA
24436851 AACAC
1 AACAC
24436856 GGTCGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.27, G:0.20, T:0.00
Consensus pattern (13 bp):
AACACAAGGCAGA
Found at i:24438393 original size:25 final size:25
Alignment explanation
Indices: 24438365--24438428 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
24438355 TACTCTCTCG
* **
24438365 AGTCATATAACAGGATGCTTATGTA
1 AGTCATATAACAGGAAGCTTATCCA
* *
24438390 AGTCATGTAACACGAAGCTTATCCA
1 AGTCATATAACAGGAAGCTTATCCA
24438415 AG--ATATAACAGGAA
1 AGTCATATAACAGGAA
24438429 ACTCATAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 10 0.31
25 22 0.69
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (25 bp):
AGTCATATAACAGGAAGCTTATCCA
Found at i:24446472 original size:21 final size:21
Alignment explanation
Indices: 24446430--24446472 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
24446420 ATCATTAATT
*
24446430 AAAAATAATAAAATATTTTTA
1 AAAAATAATAAAATATTGTTA
24446451 AAAAATAATAAAA-ATGTGTTA
1 AAAAATAATAAAATAT-TGTTA
24446472 A
1 A
24446473 TATCTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAATAATAAAATATTGTTA
Found at i:24446590 original size:30 final size:30
Alignment explanation
Indices: 24446551--24446607 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
24446541 TTTTATAAAT
24446551 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
24446581 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
24446608 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:24455566 original size:6 final size:6
Alignment explanation
Indices: 24455557--24455586 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24455547 TTAAAAATAT
*
24455557 TTTTTA TTTTAA TTTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
24455587 AAAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:24459583 original size:14 final size:14
Alignment explanation
Indices: 24459564--24459602 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
24459554 GTATATAGTA
*
24459564 AAATATTAAAATAT
1 AAATATTAAAAGAT
24459578 AAATATTAAAAAAGAT
1 AAATATT--AAAAGAT
24459594 AAATATTAA
1 AAATATTAA
24459603 TGTTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATATTAAAAGAT
Found at i:24459595 original size:16 final size:16
Alignment explanation
Indices: 24459571--24459602 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24459561 GTAAAATATT
*
24459571 AAAATATAAATATTAA
1 AAAAGATAAATATTAA
24459587 AAAAGATAAATATTAA
1 AAAAGATAAATATTAA
24459603 TGTTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAAGATAAATATTAA
Found at i:24483050 original size:21 final size:21
Alignment explanation
Indices: 24483018--24483084 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
24483008 TAAATAAATT
*
24483018 AATTGAACTGACGGTTAAACT-
1 AATTGAATTGAC-GTTAAACTC
* * *
24483039 AATTAAATTGAC-TAAAAATC
1 AATTGAATTGACGTTAAACTC
*
24483059 AATTGAATTGACGATTAAACTG
1 AATTGAATTGACG-TTAAACTC
24483081 AATT
1 AATT
24483085 TTTTTATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 10 0.29
22 9 0.26
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (21 bp):
AATTGAATTGACGTTAAACTC
Found at i:24483444 original size:9 final size:9
Alignment explanation
Indices: 24483421--24483452 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
24483411 TATTTTAGAC
24483421 AATTTTTAA
1 AATTTTTAA
24483430 AA--TTTAA
1 AATTTTTAA
24483437 AATTTTTAA
1 AATTTTTAA
24483446 AATTTTT
1 AATTTTT
24483453 TTGAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTTAA
Found at i:24486402 original size:8 final size:8
Alignment explanation
Indices: 24486389--24486434 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
24486379 GTAGAATCGG
24486389 GAGTCGCC
1 GAGTCGCC
*
24486397 GAGTCGCTA
1 GAGTCGC-C
*
24486406 GAGTCACC
1 GAGTCGCC
24486414 GAGTCGCC
1 GAGTCGCC
24486422 GGAGTCGCC
1 -GAGTCGCC
24486431 GAGT
1 GAGT
24486435 ACCAGGTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 18 0.56
9 14 0.44
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.15
Consensus pattern (8 bp):
GAGTCGCC
Found at i:24486415 original size:17 final size:17
Alignment explanation
Indices: 24486389--24486434 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
24486379 GTAGAATCGG
*
24486389 GAGTCGCCGAGTCGCTA
1 GAGTCGCCGAGTCGCCA
* *
24486406 GAGTCACCGAGTCGCCG
1 GAGTCGCCGAGTCGCCA
24486423 GAGTCGCCGAGT
1 GAGTCGCCGAGT
24486435 ACCAGGTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.15
Consensus pattern (17 bp):
GAGTCGCCGAGTCGCCA
Found at i:24486859 original size:25 final size:25
Alignment explanation
Indices: 24486830--24486881 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
24486820 ATTTATTACT
24486830 TACAAATTTCTTTACACATCCAGTG
1 TACAAATTTCTTTACACATCCAGTG
24486855 TACAAATTTCTTTACACATCCAGTG
1 TACAAATTTCTTTACACATCCAGTG
24486880 TA
1 TA
24486882 AGTAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.37
Consensus pattern (25 bp):
TACAAATTTCTTTACACATCCAGTG
Found at i:24486931 original size:19 final size:15
Alignment explanation
Indices: 24486887--24486937 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
24486877 GTGTAAGTAA
24486887 AAATTTATTACTTAC
1 AAATTTATTACTTAC
24486902 AAATTTATTACTTAC
1 AAATTTATTACTTAC
*
24486917 AAATTTATTATTTAC
1 AAATTTATTACTTAC
24486932 AAATTT
1 AAATTT
24486938 CTTTACACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTATTACTTAC
Found at i:24487147 original size:17 final size:17
Alignment explanation
Indices: 24487127--24487168 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
24487117 TTTTACTAAT
24487127 ATTATAATTTTTTCATC
1 ATTATAATTTTTTCATC
24487144 ATTATAATTTTTTCATC
1 ATTATAATTTTTTCATC
24487161 ATTATAAT
1 ATTATAAT
24487169 ATCAAGGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATAATTTTTTCATC
Found at i:24490095 original size:17 final size:17
Alignment explanation
Indices: 24490073--24490209 Score: 69
Period size: 17 Copynumber: 7.4 Consensus size: 17
24490063 AATTCAAGAC
24490073 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* *
24490090 TTATGTAGTGTTAATTCAAAA
1 TTATGTAATGTT--TT--TAA
24490111 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
* ***
24490129 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
24490148 CTTATGTAATAG-TTTTAA
1 -TTATGTAAT-GTTTTTAA
* **
24490166 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTTTTA-A
*
24490185 TTTATGTAATGCTTTTAA
1 -TTATGTAATGTTTTTAA
24490203 TTATGTA
1 TTATGTA
24490210 GTGATTTAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
16 1 0.01
17 35 0.40
18 10 0.11
19 9 0.10
20 19 0.22
21 3 0.03
22 11 0.12
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.49
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:24490116 original size:22 final size:22
Alignment explanation
Indices: 24490059--24490123 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
24490049 GTCAATTATG
*
24490059 TGTTAATTCAAGACTTATGTAA
1 TGTTAATTCAAAACTTATGTAA
* *
24490081 TGTT--TT--TAA-TTATGTAG
1 TGTTAATTCAAAACTTATGTAA
24490098 TGTTAATTCAAAACTTATGTAA
1 TGTTAATTCAAAACTTATGTAA
24490120 TGTT
1 TGTT
24490124 TTTAATTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 11 0.33
18 1 0.03
19 2 0.06
20 2 0.06
21 2 0.06
22 15 0.45
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (22 bp):
TGTTAATTCAAAACTTATGTAA
Found at i:24490218 original size:37 final size:37
Alignment explanation
Indices: 24490064--24490215 Score: 220
Period size: 37 Copynumber: 4.1 Consensus size: 37
24490054 TTATGTGTTA
24490064 ATTC-AAGACTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
24490100 TTAATTCAAA-ACTTATGTAATGTTTTTAATTATGTAGTG
1 ---ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
24490139 ATTCAAAGACTTATGTAATAG-TTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAAT-GTTTTTAATTATGTAGTG
* * *
24490176 ATTTAAAGATTTATGTAATGCTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
24490213 ATT
1 ATT
24490216 TAATTCGGGT
Statistics
Matches: 107, Mismatches: 2, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
36 8 0.07
37 63 0.59
38 1 0.01
39 33 0.31
40 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
Found at i:24490234 original size:9 final size:9
Alignment explanation
Indices: 24490216--24490305 Score: 117
Period size: 9 Copynumber: 9.6 Consensus size: 9
24490206 TGTAGTGATT
24490216 TAATTCGGG
1 TAATTCGGG
*
24490225 TAATTTGGG
1 TAATTCGGG
24490234 TAATTTTCGGG
1 TAA--TTCGGG
24490245 TAATTCGGG
1 TAATTCGGG
*
24490254 TAATTTGGG
1 TAATTCGGG
24490263 TAATTTTCGGG
1 TAA--TTCGGG
24490274 TAATTCGGG
1 TAATTCGGG
24490283 TAATTCGGG
1 TAATTCGGG
*
24490292 TAAGTCGGG
1 TAATTCGGG
24490301 TAATT
1 TAATT
24490306 TTTAACCAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
9 55 0.77
11 16 0.23
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (9 bp):
TAATTCGGG
Found at i:24490258 original size:29 final size:29
Alignment explanation
Indices: 24490216--24490294 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
24490206 TGTAGTGATT
24490216 TAATTCGGGTAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTTGGGTAATTTTCGGG
24490245 TAATTCGGGTAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTTGGGTAATTTTCGGG
*
24490274 TAATTCGGGTAATTCGGGTAA
1 TAATTCGGGTAATTTGGGTAA
24490295 GTCGGGTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (29 bp):
TAATTCGGGTAATTTGGGTAATTTTCGGG
Found at i:24490264 original size:38 final size:37
Alignment explanation
Indices: 24490216--24490306 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 37
24490206 TGTAGTGATT
24490216 TAATTCGGGTAATTT-GGGTAATTTTCGGGTAATTCGGG
1 TAATTCGGGTAATTTCGGGTAA--TTCGGGTAATTCGGG
*
24490254 TAATTTGGGTAATTTTCGGGTAATTCGGGTAATTCGGG
1 TAATTCGGGTAA-TTTCGGGTAATTCGGGTAATTCGGG
*
24490292 TAAGTCGGGTAATTT
1 TAATTCGGGTAATTT
24490307 TTAACCAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
37 3 0.06
38 36 0.75
39 3 0.06
40 6 0.12
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.40
Consensus pattern (37 bp):
TAATTCGGGTAATTTCGGGTAATTCGGGTAATTCGGG
Found at i:24491950 original size:16 final size:16
Alignment explanation
Indices: 24491919--24491955 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
24491909 ATGTGAATAA
24491919 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
24491935 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
24491951 TATTA
1 TATTA
24491956 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:24491964 original size:18 final size:18
Alignment explanation
Indices: 24491941--24492026 Score: 56
Period size: 18 Copynumber: 4.7 Consensus size: 18
24491931 TTATTATTTT
24491941 TAAAATTTATTATTAAAA
1 TAAAATTTATTATTAAAA
*
24491959 TAAAATTTAAATATT-AAA
1 TAAAATTT-ATTATTAAAA
24491977 T--AATTTATTA--AAAA
1 TAAAATTTATTATTAAAA
* *
24491991 TAATAAATTATATTAATTATAT
1 T-A-AAATT-TATT-ATTAAAA
24492013 TAATAATTTATTAT
1 TAA-AATTTATTAT
24492027 ATGACTAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 5 0.09
18 16 0.30
19 11 0.21
20 6 0.11
21 5 0.09
22 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATTTATTATTAAAA
Found at i:24492106 original size:9 final size:9
Alignment explanation
Indices: 24492092--24492116 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24492082 ATTTTATATT
24492092 AATATTTGA
1 AATATTTGA
24492101 AATATTTGA
1 AATATTTGA
24492110 AATATTT
1 AATATTT
24492117 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (9 bp):
AATATTTGA
Found at i:24493134 original size:21 final size:20
Alignment explanation
Indices: 24493106--24493144 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
24493096 ATTCATGCTA
24493106 TATTATAAAAATAATATATT
1 TATTATAAAAATAATATATT
*
24493126 TATTCATAAAAATATTATA
1 TATT-ATAAAAATAATATA
24493145 GTTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTATAAAAATAATATATT
Found at i:24497941 original size:14 final size:16
Alignment explanation
Indices: 24497915--24497948 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
24497905 ATTGTTTGGA
24497915 TATTGTATAATTTT-T
1 TATTGTATAATTTTGT
24497930 TATTGT-TAATTTTGT
1 TATTGTATAATTTTGT
24497945 TATT
1 TATT
24497949 ATTTTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (16 bp):
TATTGTATAATTTTGT
Found at i:24501304 original size:20 final size:21
Alignment explanation
Indices: 24501278--24501323 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
24501268 AGCCGGGATC
24501278 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
*
24501299 -CTAACTAATACTAATTTAAT
1 ACTAACTAATACTAATCTAAT
24501319 ACTAA
1 ACTAA
24501324 TAGAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:24501320 original size:11 final size:11
Alignment explanation
Indices: 24501278--24501324 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
24501268 AGCCGGGATC
24501278 ACTAA-CTAAT
1 ACTAATCTAAT
24501288 ACTAATCTAAT
1 ACTAATCTAAT
24501299 -CTAA-CTAAT
1 ACTAATCTAAT
*
24501308 ACTAATTTAAT
1 ACTAATCTAAT
24501319 ACTAAT
1 ACTAAT
24501325 AGAATAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
9 5 0.15
10 13 0.39
11 15 0.45
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:24501340 original size:27 final size:27
Alignment explanation
Indices: 24501305--24501360 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
24501295 TAATCTAACT
*
24501305 AATACTAATTTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
* *
24501332 AATATTAATCTAATACTAATATAATAG
1 AATACTAATCTAATACTAATAGAATAG
24501359 AA
1 AA
24501361 AAAAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:24501346 original size:11 final size:11
Alignment explanation
Indices: 24501284--24501357 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
24501274 GATCACTAAC
*
24501284 TAATACTAATC
1 TAATACTAATA
*
24501295 TAAT-CTAA-C
1 TAATACTAATA
*
24501304 TAATACTAATT
1 TAATACTAATA
24501315 TAATACTAATA
1 TAATACTAATA
* *
24501326 GAATA-GAATA
1 TAATACTAATA
24501336 TTAAT-CTAATA
1 -TAATACTAATA
24501347 CTAATA-TAATA
1 -TAATACTAATA
24501358 GAAAAAAAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 5 0.10
10 12 0.24
11 34 0.67
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (11 bp):
TAATACTAATA
Found at i:24502022 original size:14 final size:16
Alignment explanation
Indices: 24501983--24502017 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
24501973 TTTAATGTGT
*
24501983 TATAAATTACATAATA
1 TATAAAATACATAATA
24501999 TATAAAAATACATAATA
1 TAT-AAAATACATAATA
24502016 TA
1 TA
24502018 AAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TATAAAATACATAATA
Found at i:24504454 original size:20 final size:20
Alignment explanation
Indices: 24504416--24504472 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
24504406 GATGCACCCG
* *
24504416 ATTGCACTCTGGTGTCCCTA
1 ATTGCACTTTGGTGCCCCTA
* *
24504436 ATTGCACTTTCGTGCCCCTG
1 ATTGCACTTTGGTGCCCCTA
*
24504456 TTTGCACTTTGGTGCCC
1 ATTGCACTTTGGTGCCC
24504473 ATATATGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTGCACTTTGGTGCCCCTA
Found at i:24506476 original size:25 final size:25
Alignment explanation
Indices: 24506417--24506480 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
24506407 CACACCACAA
*
24506417 CTCGTATGAGCTTA-TCGATTTTAG
1 CTCGTATGAGCTTACTCGATTTCAG
24506441 CTCGTGA-GAGCTTACT-GATTTACAG
1 CTCGT-ATGAGCTTACTCGATTT-CAG
24506466 CTCGTATGAGCTTAC
1 CTCGTATGAGCTTAC
24506481 AAATATTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
24 18 0.51
25 17 0.49
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (25 bp):
CTCGTATGAGCTTACTCGATTTCAG
Found at i:24506491 original size:25 final size:23
Alignment explanation
Indices: 24506417--24506505 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 23
24506407 CACACCACAA
*
24506417 CTCGTATGAGCTTATCGATTTTAG
1 CTCGTATGAGCTTA-CGATTTCAG
24506441 CTCGTGA-GAGCTTACTGATTTACAG
1 CTCGT-ATGAGCTTAC-GATTT-CAG
*
24506466 CTCGTATGAGCTTACAAATATTCAG
1 CTCGTATGAGCTTAC-GAT-TTCAG
* *
24506491 CTCGAAGGAGCTTAC
1 CTCGTATGAGCTTAC
24506506 CGTTTATTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
23 1 0.02
24 18 0.33
25 34 0.62
26 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (23 bp):
CTCGTATGAGCTTACGATTTCAG
Found at i:24506653 original size:9 final size:9
Alignment explanation
Indices: 24506639--24506663 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24506629 GTTTTCGAAC
24506639 TCGAATAAT
1 TCGAATAAT
24506648 TCGAATAAT
1 TCGAATAAT
24506657 TCGAATA
1 TCGAATA
24506664 TCAAACTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (9 bp):
TCGAATAAT
Found at i:24508948 original size:40 final size:40
Alignment explanation
Indices: 24508893--24508974 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
24508883 TTACAAATGG
24508893 TTATTGTGTTGCATTAGAAGATGTTTAACTATGTGTTGTT
1 TTATTGTGTTGCATTAGAAGATGTTTAACTATGTGTTGTT
24508933 TTATTGTGTTGCATTAGAAGATGTTTAACTATGTGTTGTT
1 TTATTGTGTTGCATTAGAAGATGTTTAACTATGTGTTGTT
24508973 TT
1 TT
24508975 CTTTTAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (40 bp):
TTATTGTGTTGCATTAGAAGATGTTTAACTATGTGTTGTT
Found at i:24510038 original size:2 final size:2
Alignment explanation
Indices: 24510031--24510067 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
24510021 AAAGTTAAGA
*
24510031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24510068 ACCCCATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:24514941 original size:63 final size:63
Alignment explanation
Indices: 24514842--24514967 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
24514832 TATGGGATAC
24514842 CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
1 CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
* *
24514905 CTACAAAGGGAAATTCAGAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
1 CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
24514968 TAGAGATCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.20
Consensus pattern (63 bp):
CTACAAAGGGAAAATCAAAGAAAATGAACACTTGTCGTAATACCCTTTAAAGAGAAAAGATCA
Found at i:24515922 original size:26 final size:26
Alignment explanation
Indices: 24515885--24515946 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
24515875 CATTTGATAG
24515885 TCCTAG-TTTTCGACGACTGTCTCTT
1 TCCTAGATTTTCGACGACTGTCTCTT
*
24515910 TCCTAGATTTTCGACGATTGTCTCTT
1 TCCTAGATTTTCGACGACTGTCTCTT
24515936 TCCTAGATTTT
1 TCCTAGATTTT
24515947 TCTTATTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (26 bp):
TCCTAGATTTTCGACGACTGTCTCTT
Found at i:24517782 original size:25 final size:25
Alignment explanation
Indices: 24517740--24517819 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
24517730 AGCCCTCTCT
* * *
24517740 CGAGCCATATAATAGGAAGCTCATG
1 CGAGCTATATAATGGGAAGCTCATC
* * * *
24517765 TGAGTTATGTAATGGGAAGCTTATC
1 CGAGCTATATAATGGGAAGCTCATC
* *
24517790 CGAGCTATATAACGGGAAGCTCATA
1 CGAGCTATATAATGGGAAGCTCATC
24517815 CGAGC
1 CGAGC
24517820 CAATAACAGG
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (25 bp):
CGAGCTATATAATGGGAAGCTCATC
Found at i:24525993 original size:9 final size:9
Alignment explanation
Indices: 24525975--24526060 Score: 102
Period size: 9 Copynumber: 9.4 Consensus size: 9
24525965 TTTGGTTAAA
*
24525975 AATTATCCG
1 AATTACCCG
24525984 AATTACCCG
1 AATTACCCG
*
24525993 AATTATCCG
1 AATTACCCG
24526002 AATTACCCG
1 AATTACCCG
*
24526011 AATTAACCG
1 AATTACCCG
*
24526020 AATTAACCG
1 AATTACCCG
24526029 AATTA-CCG
1 AATTACCCG
*
24526037 AAAAATACCCG
1 --AATTACCCG
24526048 AATTACCCG
1 AATTACCCG
24526057 AATT
1 AATT
24526061 TTTTTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.85
10 4 0.06
11 3 0.04
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:24530188 original size:40 final size:41
Alignment explanation
Indices: 24530126--24530241 Score: 114
Period size: 40 Copynumber: 2.9 Consensus size: 41
24530116 GTTTGGAACA
* *
24530126 AAAGCGCCAC-AACAAATCGAGCATTAGCGGCGATTTAGCC-
1 AAAGCGCCGCTAA-AAATAGAGCATTAGCGGCGATTTAGCCG
** * *
24530166 AAAGCGCCGCTAAAGGTAGAGCATCAGCGGCGA-TTATCCG
1 AAAGCGCCGCTAAAAATAGAGCATTAGCGGCGATTTAGCCG
* * *
24530206 GAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTA
1 AAAGCGCCGCTAAAAATAGAGCATTAGCGGCGATTTA
24530242 TATAAAGCGC
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
39 15 0.25
40 44 0.72
41 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (41 bp):
AAAGCGCCGCTAAAAATAGAGCATTAGCGGCGATTTAGCCG
Found at i:24530356 original size:41 final size:41
Alignment explanation
Indices: 24530299--24530618 Score: 297
Period size: 41 Copynumber: 7.8 Consensus size: 41
24530289 TATGTTAAAC
* *
24530299 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCTGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
*
24530340 CTTTAGAGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
*
24530381 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
*
24530422 CTTTAGCGGCGTTTTTATAC-AAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTCGGAT
* * ** * * * *
24530463 CTTTCGCGGCGTTTCTAACTGAGCGCCACTAATTCTCTTG-T
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GGAT
* * * ** * * * * *
24530504 CTTCAGCGACGTTTCTAACTGAGTGCCACTAATTCTCTTG-T
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GGAT
* * * ** *
24530545 CTTCAGCGGCGTTTGTATCTAAGCGCCGCTAATG-TATTGAC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGAT
* *
24530586 CTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
24530619 AGTAACAAAT
Statistics
Matches: 242, Mismatches: 32, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.02
41 236 0.98
42 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
Found at i:24531082 original size:15 final size:15
Alignment explanation
Indices: 24531061--24531098 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
24531051 TTTATGGTTA
24531061 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
24531076 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
24531091 ATTTAGGG
1 ATTTAGGG
24531099 TTAATTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:24531793 original size:2 final size:2
Alignment explanation
Indices: 24531786--24531822 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24531776 ATAATTATTA
24531786 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
24531823 ATAGGTGCGT
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:24532511 original size:38 final size:37
Alignment explanation
Indices: 24532427--24532517 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 37
24532417 AAATTTGATG
* *
24532427 TTTAGGGGTTAGGGGGATTTAGGGTTTAAGGGGTATGC
1 TTTAGGGGTTA-GGGGATTTAGGGTGTAAGGGGTATGA
24532465 TTTAGGGGTTAGGGGATTTAGGG-GTAAGGGGGTTATGGA
1 TTTAGGGGTTAGGGGATTTAGGGTGTAA-GGGG-TAT-GA
24532504 TTT-GGGGTTTAGGG
1 TTTAGGGG-TTAGGG
24532518 TTTCAACCGT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
36 3 0.06
37 16 0.34
38 18 0.38
39 10 0.21
ACGTcount: A:0.18, C:0.01, G:0.47, T:0.34
Consensus pattern (37 bp):
TTTAGGGGTTAGGGGATTTAGGGTGTAAGGGGTATGA
Found at i:24532517 original size:23 final size:24
Alignment explanation
Indices: 24532465--24532517 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
24532455 AGGGGTATGC
24532465 TTTA-GGGGTTAGGGGATTTAGGG
1 TTTAGGGGGTTAGGGGATTTAGGG
* * * *
24532488 GTAAGGGGGTTA-TGGATTTGGGG
1 TTTAGGGGGTTAGGGGATTTAGGG
24532511 TTTAGGG
1 TTTAGGG
24532518 TTTCAACCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.17, C:0.00, G:0.49, T:0.34
Consensus pattern (24 bp):
TTTAGGGGGTTAGGGGATTTAGGG
Found at i:24535673 original size:25 final size:22
Alignment explanation
Indices: 24535644--24535697 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
24535634 TTACATAAAT
24535644 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
24535669 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
24535691 TACATAA
1 TACATAA
24535698 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:24535687 original size:22 final size:22
Alignment explanation
Indices: 24535659--24535704 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
24535649 AACTTAGTTA
*
24535659 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
24535681 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
24535703 AT
1 AT
24535705 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:24535708 original size:56 final size:56
Alignment explanation
Indices: 24535635--24536085 Score: 713
Period size: 56 Copynumber: 7.8 Consensus size: 56
24535625 ATACATAAAT
24535635 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
24535691 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
24535747 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
* * * *
24535803 TACATAAATTACATAACTTAATTAGTTAAGATACATAAATCACATAACATACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATT-A-AT--AT-TAT-ACATAACTTACATTAATATTA
24535865 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
*
24535921 TACATACATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
* * * *
24535977 TACATAAATTACATAACTTAATTAGTTAATATACATAAATTGCATAACATACATTAATATTA
1 TACATAAATTACATAACTTAGTTAATTAATAT---T--A-TACATAACTTACATTAATATTA
24536039 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACA
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACA
24536086 ACTTACATAA
Statistics
Matches: 365, Mismatches: 18, Indels: 24
0.90 0.04 0.06
Matches are distributed among these distances:
56 252 0.69
57 4 0.01
58 4 0.01
59 2 0.01
60 4 0.01
61 4 0.01
62 95 0.26
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (56 bp):
TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
Found at i:24535728 original size:25 final size:22
Alignment explanation
Indices: 24535700--24535753 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
24535690 ATACATAAAT
24535700 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
24535725 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
24535747 TACATAA
1 TACATAA
24535754 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:24535743 original size:22 final size:22
Alignment explanation
Indices: 24535715--24535760 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
24535705 AACTTAGTTA
*
24535715 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
24535737 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
24535759 AT
1 AT
24535761 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:24535784 original size:25 final size:22
Alignment explanation
Indices: 24535756--24535809 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
24535746 ATACATAAAT
24535756 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
24535781 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
24535803 TACATAA
1 TACATAA
24535810 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:24535799 original size:22 final size:22
Alignment explanation
Indices: 24535771--24535816 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
24535761 AACTTAGTTA
*
24535771 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
24535793 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
24535815 AT
1 AT
24535817 AACTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:24535902 original size:25 final size:22
Alignment explanation
Indices: 24535874--24535926 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
24535864 ATACATAAAT
24535874 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
24535899 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
24535921 TACATA
1 TACATA
24535927 CATTACATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 16 0.59
25 11 0.41
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:24535909 original size:174 final size:172
Alignment explanation
Indices: 24535635--24536085 Score: 784
Period size: 174 Copynumber: 2.6 Consensus size: 172
24535625 ATACATAAAT
* * * *
24535635 TACATAAATTACATAACTTAGTTAATT-AAT--AT-TATACATAACTTACATTAATATTATACAT
1 TACATAAATTACATAACTTAATTAGTTAAATACATAAATACATAACATACATTAATATTATACAT
24535696 AAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAATTACAT
66 AAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAATTACAT
24535761 AACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
131 AACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
24535803 TACATAAATTACATAACTTAATTAGTTAAGATACATAAATCACATAACATACATTAATATTATAC
1 TACATAAATTACATAACTTAATTAGTTAA-ATACATAAAT-ACATAACATACATTAATATTATAC
*
24535868 ATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATACATTAC
64 ATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAATTAC
24535933 ATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
129 ATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
*
24535977 TACATAAATTACATAACTTAATTAGTTAATATACATAAATTGCATAACATACATTAATATTATAC
1 TACATAAATTACATAACTTAATTAGTTAA-ATACATAAA-TACATAACATACATTAATATTATAC
24536042 ATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACA
64 ATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACA
24536086 ACTTACATAA
Statistics
Matches: 269, Mismatches: 7, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
168 25 0.09
169 1 0.00
170 2 0.01
172 2 0.01
173 2 0.01
174 236 0.88
175 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (172 bp):
TACATAAATTACATAACTTAATTAGTTAAATACATAAATACATAACATACATTAATATTATACAT
AAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAATTACAT
AACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
Found at i:24535917 original size:22 final size:22
Alignment explanation
Indices: 24535889--24535934 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
24535879 AACTTAGTTA
24535889 ATTAATATTATACATA-ACTTAC
1 ATTAATATTATACATACA-TTAC
24535911 ATTAATATTATACATACATTAC
1 ATTAATATTATACATACATTAC
24535933 AT
1 AT
24535935 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATACATTAC
Found at i:24535920 original size:118 final size:112
Alignment explanation
Indices: 24535635--24536085 Score: 713
Period size: 118 Copynumber: 3.9 Consensus size: 112
24535625 ATACATAAAT
24535635 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
24535700 TACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
66 TACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
24535747 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
* * * *
24535812 TACATAACTTAATTAGTTAAGATACATAAATCACATAACATACATTAATATTA
66 TACATAACTTAGTTAATT-A-AT--AT-TAT-ACATAACTTACATTAATATTA
*
24535865 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATACAT
1 TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
24535930 TACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
66 TACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
* * * *
24535977 TACATAAATTACATAACTTAATTAGTTAATATACATAAATTGCATAACATACATTAATATTATAC
1 TACATAAATTACATAACTTAGTTAATTAATAT---T--A-TACATAACTTACATTAATATTATAC
24536042 ATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACA
60 ATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACA
24536086 ACTTACATAA
Statistics
Matches: 313, Mismatches: 14, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
112 131 0.42
113 3 0.01
114 4 0.01
115 1 0.00
116 4 0.01
117 4 0.01
118 166 0.53
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (112 bp):
TACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
TACATAACTTAGTTAATTAATATTATACATAACTTACATTAATATTA
Found at i:24535958 original size:25 final size:22
Alignment explanation
Indices: 24535930--24535983 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
24535920 ATACATACAT
24535930 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
24535955 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
24535977 TACATAA
1 TACATAA
24535984 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:24535973 original size:22 final size:22
Alignment explanation
Indices: 24535945--24535990 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
24535935 AACTTAGTTA
*
24535945 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
24535967 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
24535989 AT
1 AT
24535991 AACTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:24536097 original size:9 final size:9
Alignment explanation
Indices: 24536039--24536189 Score: 63
Period size: 9 Copynumber: 17.3 Consensus size: 9
24536029 ATTAATATTA
*
24536039 TACATAAAT
1 TACATAACT
24536048 TACATAACT
1 TACATAACT
**
24536057 TAGTTAA-T
1 TACATAACT
*
24536065 TA-AT-ATT
1 TACATAACT
24536072 ATACATAACT
1 -TACATAACT
24536082 TAC--AACT
1 TACATAACT
24536089 TACATAACT
1 TACATAACT
* **
24536098 TATACGACT
1 TACATAACT
24536107 TACATAACT
1 TACATAACT
24536116 TACATAGCATACTT
1 TACAT---A-AC-T
*
24536130 TTCATAA--
1 TACATAACT
*
24536137 TACACAACT
1 TACATAACT
*
24536146 TACATAATT
1 TACATAACT
*
24536155 TTCATAA--
1 TACATAACT
*
24536162 TAAATAACT
1 TACATAACT
24536171 TACATAA--
1 TACATAACT
24536178 TACATAACT
1 TACATAACT
24536187 TAC
1 TAC
24536190 GTAGCTTAAT
Statistics
Matches: 105, Mismatches: 20, Indels: 34
0.66 0.13 0.21
Matches are distributed among these distances:
6 1 0.01
7 26 0.25
8 5 0.05
9 61 0.58
10 3 0.03
11 1 0.01
12 1 0.01
13 2 0.02
14 5 0.05
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:24536151 original size:25 final size:25
Alignment explanation
Indices: 24536123--24536178 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
24536113 ACTTACATAG
* *
24536123 CATACTTTTCATAATACACAACTTA
1 CATAATTTTCATAATAAACAACTTA
*
24536148 CATAATTTTCATAATAAATAACTTA
1 CATAATTTTCATAATAAACAACTTA
24536173 CATAAT
1 CATAAT
24536179 ACATAACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.38
Consensus pattern (25 bp):
CATAATTTTCATAATAAACAACTTA
Found at i:24536168 original size:16 final size:16
Alignment explanation
Indices: 24536157--24536189 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24536147 ACATAATTTT
24536157 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
24536173 CATAATACATAACTTA
1 CATAATAAATAACTTA
24536189 C
1 C
24536190 GTAGCTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:24538033 original size:21 final size:22
Alignment explanation
Indices: 24537987--24538033 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
24537977 TAGAAGATCA
**
24537987 AATGATGAAGCTGATGATAACT
1 AATGATGAAGAGGATGATAACT
*
24538009 -ATGATGAAGAGGATGAT-CCT
1 AATGATGAAGAGGATGATAACT
24538029 AATGA
1 AATGA
24538034 GGCGGACTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (22 bp):
AATGATGAAGAGGATGATAACT
Found at i:24541801 original size:66 final size:65
Alignment explanation
Indices: 24541694--24541864 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
24541684 GAGCAAATTA
* * * *
24541694 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
24541758 G
65 G
* *
24541759 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
24541824 G
65 G
* ** * *
24541825 CAGCAGCTTAAAGCAGATGTGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
24541865 CGGTAGTGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:24541959 original size:26 final size:21
Alignment explanation
Indices: 24541890--24541947 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
24541880 TATAGGTTGC
24541890 AGCGAGGGAAGCAGAGGCTAA
1 AGCGAGGGAAGCAGAGGCTAA
*
24541911 AGGGAGGGAAGCAGAGGCTAA
1 AGCGAGGGAAGCAGAGGCTAA
24541932 AGCGAGGGAAGCAGAG
1 AGCGAGGGAAGCAGAG
24541948 CAGCGTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.47, T:0.03
Consensus pattern (21 bp):
AGCGAGGGAAGCAGAGGCTAA
Found at i:24542321 original size:43 final size:43
Alignment explanation
Indices: 24542274--24542566 Score: 272
Period size: 43 Copynumber: 6.8 Consensus size: 43
24542264 GTTTTTGGTT
*
24542274 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTAGAA
1 AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTAGAA
* * * **
24542317 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGG
1 AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTAGAA
* * * * **
24542360 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTCGTC
1 AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTAGAA
* *
24542403 AAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTG-AGAGG
1 AAAGCGCCGCTAAAGATCAGGGTCT-TTAGCGGCGTTTGTAGA-A
* *
24542446 AAAGCGCCGCTAAAGAAT-AGGTTCTTTAGTGGCGTTTG-AGGAGA
1 AAAGCGCCGCTAAAG-ATCAGGGTCTTTAGCGGCGTTTGTA-GA-A
* * ** * * * **
24542490 AAAACGCCGCTAAAGACCTTGATCTTTAGCGGCGCTTCTCCCAA
1 AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT-AGAA
24542534 AAA-CGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCG
24542567 CTTCCACTAA
Statistics
Matches: 203, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.01
43 160 0.79
44 39 0.19
45 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTAGAA
Found at i:24542567 original size:43 final size:43
Alignment explanation
Indices: 24542278--24542613 Score: 250
Period size: 43 Copynumber: 7.8 Consensus size: 43
24542268 TTGGTTAAAG
*
24542278 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGT-AGAAAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAGAAAAA
* * ** * *
24542320 GCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGGAAAG
1 -CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAGAAAAA
* * * * *
24542364 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTC-GTCAAAG
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAG-AAAAA
* ** * *
24542407 CGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGAGGAAAG
1 CGCCGCTAAAGATCAGGGTCT-TTAGCGGCGTTTGTCAGAAAAA
* * **
24542450 CGCCGCTAAAGAAT-AGGTTCTTTAGTGGCGTTTGAGGAGAAAAA
1 CGCCGCTAAAG-ATCAGGGTCTTTAGCGGCGTTTG-TCAGAAAAA
* ** * * * **
24542494 CGCCGCTAAAGACCTTGATCTTTAGCGGCGCTTCTCCCAAAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAGAAAAA
* * **
24542537 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTT-CCACTAAAA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAGAAAAA
* *** *
24542579 CGCCGCTAAAGGTCTTAGTCTTCAGCGGCGTTTGT
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGT
24542614 GCTAGAAGCG
Statistics
Matches: 233, Mismatches: 51, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
42 36 0.15
43 157 0.67
44 40 0.17
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (43 bp):
CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCAGAAAAA
Found at i:24542743 original size:22 final size:22
Alignment explanation
Indices: 24542715--24542757 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24542705 TTGCGGCGCT
*
24542715 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
24542737 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
24542758 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:24547794 original size:22 final size:22
Alignment explanation
Indices: 24547768--24547810 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24547758 AGCAAAGATC
* *
24547768 AAAACGTGCTACAAAGTAGAGG
1 AAAACATGCTACAAAGCAGAGG
24547790 AAAACATGCTACAAAGCAGAG
1 AAAACATGCTACAAAGCAGAG
24547811 TGATTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (22 bp):
AAAACATGCTACAAAGCAGAGG
Found at i:24549429 original size:22 final size:21
Alignment explanation
Indices: 24549385--24549430 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
24549375 TACTCTCAAA
* *
24549385 TTTTCACTTTTTCTTCAATAT
1 TTTTCACTTTTTATTCAAAAT
*
24549406 TTTTCACATTTTTATTTAAAAT
1 TTTTCAC-TTTTTATTCAAAAT
24549428 TTT
1 TTT
24549431 AATTTCCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTCACTTTTTATTCAAAAT
Found at i:24549430 original size:21 final size:20
Alignment explanation
Indices: 24549382--24549430 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
24549372 CTCTACTCTC
*
24549382 AAATTTTCACTTTTTCTTCA
1 AAATTTTCACTTTTTATTCA
* *
24549402 ATATTTTTCACATTTTTATTTA
1 A-AATTTTCAC-TTTTTATTCA
24549424 AAATTTT
1 AAATTTT
24549431 AATTTCCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATTTTCACTTTTTATTCA
Found at i:24554199 original size:5 final size:5
Alignment explanation
Indices: 24554173--24554251 Score: 58
Period size: 5 Copynumber: 15.6 Consensus size: 5
24554163 TTCTTTTGAT
*
24554173 ATATA TATATA TATAAA ATATA ATATA ATAT- AT-TA ATAATA ATATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
* *
24554219 ATATA A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA ATATA AT-A-TA ATATA ATATA ATA
24554252 ATATTTTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.05
4 6 0.10
5 33 0.54
6 16 0.26
7 3 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:24554203 original size:19 final size:19
Alignment explanation
Indices: 24554171--24554233 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
24554161 CTTTCTTTTG
24554171 ATAT-ATATATATATATAAA
1 ATATAATATA-ATATATAAA
*
24554190 ATATAATATAATATAT-TA
1 ATATAATATAATATATAAA
24554208 ATAATAATATAATATA-AAA
1 AT-ATAATATAATATATAAA
*
24554227 ACATAAT
1 ATATAAT
24554234 CATTACTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.21
19 25 0.66
20 5 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATATAATATATAAA
Found at i:24554233 original size:24 final size:24
Alignment explanation
Indices: 24554185--24554252 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
24554175 ATATATATAT
* *
24554185 ATAA-AATATAATATAATATATTA
1 ATAATAATATAATATAATAAAATA
24554208 ATAATAATATAATATAA-AAACATA
1 ATAATAATATAATATAATAAA-ATA
* *
24554232 ATCATTACTATAATATAATAA
1 AT-AATAATATAATATAATAA
24554253 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.16
24 16 0.43
25 13 0.35
26 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATAATATAATATAATAAAATA
Found at i:24558061 original size:20 final size:20
Alignment explanation
Indices: 24558033--24558079 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
24558023 TAGATACAAA
* *
24558033 TTTAATTTT-AGTTATTTTAT
1 TTTATTTTTCAGTTA-TTAAT
*
24558053 TTTATTTTTCGGTTATTAAT
1 TTTATTTTTCAGTTATTAAT
24558073 TTTATTT
1 TTTATTT
24558080 CAATTTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTATTTTTCAGTTATTAAT
Found at i:24558366 original size:48 final size:48
Alignment explanation
Indices: 24558295--24558391 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
24558285 GTCACTTCTC
24558295 ATAAATTATTATCTTAAATTGTTTCTGGTGTAAACATTATAAAACCTT
1 ATAAATTATTATCTTAAATTGTTTCTGGTGTAAACATTATAAAACCTT
24558343 ATAAATTATTATCTTAAATTGTTTCTGGTGTAAACATTATAAAACCTT
1 ATAAATTATTATCTTAAATTGTTTCTGGTGTAAACATTATAAAACCTT
24558391 A
1 A
24558392 GTGTTTGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.43
Consensus pattern (48 bp):
ATAAATTATTATCTTAAATTGTTTCTGGTGTAAACATTATAAAACCTT
Found at i:24561274 original size:7 final size:7
Alignment explanation
Indices: 24561262--24561290 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
24561252 ATGAAATTAA
24561262 CGAGATT
1 CGAGATT
24561269 CGAGATT
1 CGAGATT
24561276 CGAGATT
1 CGAGATT
24561283 CGAGATT
1 CGAGATT
24561290 C
1 C
24561291 AATAGGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (7 bp):
CGAGATT
Found at i:24565904 original size:29 final size:29
Alignment explanation
Indices: 24565865--24566023 Score: 176
Period size: 29 Copynumber: 5.5 Consensus size: 29
24565855 TCCGAAAATA
*
24565865 GCCACAAAGGCTTCCTTTTAATAGAGATC
1 GCCACAAAGGCTTCCTTATAATAGAGATC
* * *
24565894 CCCCCAAAGGCTTCCTTATAACAGAGATC
1 GCCACAAAGGCTTCCTTATAATAGAGATC
* * * *
24565923 GCCATAAAGGCTTCCTTATAACAAAGATA
1 GCCACAAAGGCTTCCTTATAATAGAGATC
* * * *
24565952 GCTAAAAAGACATT-CTTTTAATAGAGATC
1 GCCACAAAGGC-TTCCTTATAATAGAGATC
*
24565981 GCCACAAAGGCTTCCTTATAATAGAGGTC
1 GCCACAAAGGCTTCCTTATAATAGAGATC
*
24566010 ACCACAAAGGCTTC
1 GCCACAAAGGCTTC
24566024 TTTTCAAAGG
Statistics
Matches: 106, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 2 0.02
29 102 0.96
30 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (29 bp):
GCCACAAAGGCTTCCTTATAATAGAGATC
Done.