Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 127 of 210
Found at i:42350578 original size:38 final size:38
Alignment explanation
Indices: 42350527--42350602 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
42350517 TTATGAATAG
42350527 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
1 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
42350565 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
1 TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
42350603 GAAAGATGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (38 bp):
TAGTCAAAGTAATTGGAAAAAATGCAGATCCTTTCTTT
Found at i:42355053 original size:33 final size:34
Alignment explanation
Indices: 42354997--42355063 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
42354987 CGAACAAATG
*
42354997 GCCAAAATGAGGATTTTTTACTAAATTTATATAA
1 GCCAAAATGAGGATTTTTCACTAAATTTATATAA
42355031 GCCAAAATGAGG-TTTTTCACTAAATTTATATAA
1 GCCAAAATGAGGATTTTTCACTAAATTTATATAA
42355064 AAAACTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (34 bp):
GCCAAAATGAGGATTTTTCACTAAATTTATATAA
Found at i:42355317 original size:27 final size:27
Alignment explanation
Indices: 42355270--42355336 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
42355260 ACAAATGGGG
* * *
42355270 GGTGCCGCCTGTGGCAGTGGCACCTTT
1 GGTGCCGCCTGTGCCACTGGCACCATT
*
42355297 GGTGCCGCCTTTGCCACTGGCACCATT
1 GGTGCCGCCTGTGCCACTGGCACCATT
*
42355324 GGTACCGCCTGTG
1 GGTGCCGCCTGTG
42355337 GCGGTCCCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.09, C:0.33, G:0.33, T:0.25
Consensus pattern (27 bp):
GGTGCCGCCTGTGCCACTGGCACCATT
Found at i:42357959 original size:20 final size:20
Alignment explanation
Indices: 42357934--42357973 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42357924 GGTCAAACAT
42357934 GCACCACTTAAGCATCGATA
1 GCACCACTTAAGCATCGATA
42357954 GCACCACTTAAGCATCGATA
1 GCACCACTTAAGCATCGATA
42357974 CTTTGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (20 bp):
GCACCACTTAAGCATCGATA
Found at i:42372116 original size:28 final size:27
Alignment explanation
Indices: 42372063--42372116 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
42372053 ATGTTGAATA
*
42372063 ATAATACTTATATCTTTAATAATAATG
1 ATAATACTTATATATTTAATAATAATG
42372090 ATAATACTTATAATATTTAATAATAAT
1 ATAATACTTAT-ATATTTAATAATAAT
42372117 ACAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (27 bp):
ATAATACTTATATATTTAATAATAATG
Found at i:42372122 original size:27 final size:27
Alignment explanation
Indices: 42372065--42372122 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
42372055 GTTGAATAAT
* *
42372065 AATACTTATATCTTTAATAATAATGAT
1 AATACTTATATATTTAATAATAATGAC
42372092 AATACTTATAATATTTAATAATAAT-AC
1 AATACTTAT-ATATTTAATAATAATGAC
42372119 AATA
1 AATA
42372123 ATAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (27 bp):
AATACTTATATATTTAATAATAATGAC
Found at i:42376206 original size:29 final size:29
Alignment explanation
Indices: 42376130--42376210 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
42376120 ATTTGTTAAT
* * *
42376130 GCACTTCGGTGCCACTCTGTTTTGATAAA
1 GCACTTCGATGCCACTCTATTCTGATAAA
** * **
42376159 GCACTTCGATGTTATTCTATTCTGATATT
1 GCACTTCGATGCCACTCTATTCTGATAAA
*
42376188 GTACTTCGATGCCACTCTATTCT
1 GCACTTCGATGCCACTCTATTCT
42376211 ATGATTACAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (29 bp):
GCACTTCGATGCCACTCTATTCTGATAAA
Found at i:42377832 original size:22 final size:23
Alignment explanation
Indices: 42377806--42377849 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
42377796 AATCCTTAAA
*
42377806 AAATAAATATTAAA-ACTAAAAC
1 AAATAAATACTAAATACTAAAAC
42377828 AAATAAATACTAAATACTAAAA
1 AAATAAATACTAAATACTAAAA
42377850 TATTCATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAAATACTAAATACTAAAAC
Found at i:42390175 original size:117 final size:119
Alignment explanation
Indices: 42390024--42390263 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 119
42390014 CACTATCACA
42390024 ATAT-TATGCAAAAATATAATATGAACTACAACATAAACAAACAATTTATTTTTAAATTGAATCA
1 ATATGTATGCAAAAATATAATATGAACTACAACATAAACAAACAATTTATTTTTAAATTGAATCA
42390088 TAATAATAAATTATACAAAACACAGCATGCCAAAAATAAATAGATATTATTAAT
66 TAATAATAAATTATACAAAACACAGCATGCCAAAAATAAATAGATATTATTAAT
42390142 ATATGTATGC-AAAA-ATAATATGAACTACAACATAAACAAACAATTTATTTTTAAATTGAATCA
1 ATATGTATGCAAAAATATAATATGAACTACAACATAAACAAACAATTTATTTTTAAATTGAATCA
42390205 TAATAATAAATTATACAAAACACAGCATGCCAAAAATAAATAGATATTATTAAT
66 TAATAATAAATTATACAAAACACAGCATGCCAAAAATAAATAGATATTATTAAT
42390259 ATATG
1 ATATG
42390264 AAAATACAAA
Statistics
Matches: 121, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
117 108 0.89
118 8 0.07
119 5 0.04
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (119 bp):
ATATGTATGCAAAAATATAATATGAACTACAACATAAACAAACAATTTATTTTTAAATTGAATCA
TAATAATAAATTATACAAAACACAGCATGCCAAAAATAAATAGATATTATTAAT
Found at i:42390290 original size:23 final size:23
Alignment explanation
Indices: 42390250--42390316 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
42390240 ATAAATAGAT
* *
42390250 ATTATTAATATATGAAAATACAA
1 ATTATAAATATATAAAAATACAA
* *
42390273 ATTATAAATTTATAAAAAATATAA
1 ATTATAAATATAT-AAAAATACAA
*
42390297 ATATATAAAATGTATAAAAA
1 AT-TAT-AAATATATAAAAA
42390317 ATTTGTTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 11 0.31
24 10 0.28
25 8 0.22
26 7 0.19
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (23 bp):
ATTATAAATATATAAAAATACAA
Found at i:42390312 original size:17 final size:16
Alignment explanation
Indices: 42390271--42390314 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
42390261 ATGAAAATAC
*
42390271 AAATTATAAATTTATAA
1 AAATTATAAATATAT-A
*
42390288 AAAATATAAATATATA
1 AAATTATAAATATATA
42390304 AAATGTATAAA
1 AAAT-TATAAA
42390315 AAATTTGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATTATAAATATATA
Found at i:42401973 original size:30 final size:30
Alignment explanation
Indices: 42401939--42402042 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 30
42401929 TATCTATAAT
42401939 TAAATTTGAGGATCAAATTGATTGAATTTG
1 TAAATTTGAGGATCAAATTGATTGAATTTG
* * ** * *
42401969 TAAATGTGAAGGGTTTAATTTATTGAATTATT
1 TAAATTTG-AGGATCAAATTGATTGAATT-TG
* *
42402001 TAGAA-TT-AGGATCAAATTGATAGAATATG
1 TA-AATTTGAGGATCAAATTGATTGAATTTG
*
42402030 TAAGTATTGAGGA
1 TAAAT-TTGAGGA
42402043 CTAAATATAT
Statistics
Matches: 53, Mismatches: 15, Indels: 11
0.67 0.19 0.14
Matches are distributed among these distances:
28 1 0.02
29 3 0.06
30 23 0.43
31 20 0.38
32 4 0.08
33 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
TAAATTTGAGGATCAAATTGATTGAATTTG
Found at i:42408489 original size:29 final size:30
Alignment explanation
Indices: 42408451--42408507 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
42408441 GGGTTGGGAG
42408451 GGGAGAGGAGTAAAAGTTTTGAGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAGT
42408481 GGGA-AGGAGTAAAAGTTTTGAGGGAAA
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAA
42408508 AGTAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (30 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAGT
Found at i:42408683 original size:9 final size:9
Alignment explanation
Indices: 42408666--42408696 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42408656 TCGAGTTGAT
42408666 TCGAATAAC
1 TCGAATAAC
*
42408675 TCGATTAAC
1 TCGAATAAC
42408684 TCGAATAAC
1 TCGAATAAC
42408693 TCGA
1 TCGA
42408697 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42409629 original size:29 final size:29
Alignment explanation
Indices: 42409596--42409652 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
42409586 AGTTTTTTCA
*
42409596 GCCTAATCCTATAAATTTT-TGAAAAATAG
1 GCCTAATCCGATAAATTTTCT-AAAAATAG
*
42409625 GCCTAATTCGATAAATTTTCTAAAAATA
1 GCCTAATCCGATAAATTTTCTAAAAATA
42409653 CGACATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (29 bp):
GCCTAATCCGATAAATTTTCTAAAAATAG
Found at i:42416104 original size:18 final size:19
Alignment explanation
Indices: 42416081--42416138 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
42416071 TCCTAGACCA
42416081 TTTTTAAGGGTTT-GGATT
1 TTTTTAAGGGTTTAGGATT
*
42416099 TTTTTAAGAGTTTAAGG-TT
1 TTTTTAAGGGTTT-AGGATT
*
42416118 TTTCT-AGGGTTTAGGATT
1 TTTTTAAGGGTTTAGGATT
42416136 TTT
1 TTT
42416139 GTTTTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.09
18 23 0.68
19 6 0.18
20 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.24, T:0.55
Consensus pattern (19 bp):
TTTTTAAGGGTTTAGGATT
Found at i:42421619 original size:22 final size:22
Alignment explanation
Indices: 42421594--42421671 Score: 138
Period size: 22 Copynumber: 3.5 Consensus size: 22
42421584 TTTCACAAAC
42421594 AAATTCTCTCAATTTCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
*
42421616 AAATTCTCTCAATTCCCTTCAA
1 AAATTCTCTCAATTTCCTTCAA
*
42421638 AAATTCTCTCAATTTCCTTCCA
1 AAATTCTCTCAATTTCCTTCAA
42421660 AAATTCTCTCAA
1 AAATTCTCTCAA
42421672 ACTCTCAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTCTCTCAATTTCCTTCAA
Found at i:42421677 original size:30 final size:30
Alignment explanation
Indices: 42421643--42421701 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
42421633 TTCAAAAATT
* *
42421643 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
42421673 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
42421702 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:42421678 original size:52 final size:51
Alignment explanation
Indices: 42421621--42421723 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
42421611 TTCAAAAATT
* * *
42421621 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
42421673 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
42421724 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:42421712 original size:21 final size:22
Alignment explanation
Indices: 42421673--42421714 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42421663 TTCTCTCAAA
42421673 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
42421695 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
42421715 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:42424498 original size:23 final size:23
Alignment explanation
Indices: 42424468--42424593 Score: 117
Period size: 23 Copynumber: 5.0 Consensus size: 23
42424458 NNNNNNNCCT
42424468 TAACCTAATTTAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACCC
* * *
42424491 TAACCTAATTGAACCTAAAACCCAAACC
1 TAACCTAATTTAA--TTAAA---AACCC
*
42424519 TAACTTAATTTAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACCC
42424542 TAACCTAACTTAATTTAATTAAAAACCC
1 TAA-C---C-TAATTTAATTAAAAACCC
*
42424570 TAACCTAATTGAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACCC
42424593 T
1 T
42424594 NNNNNNNNNN
Statistics
Matches: 84, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
23 37 0.44
24 2 0.02
25 4 0.05
26 4 0.05
27 1 0.01
28 36 0.43
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.29
Consensus pattern (23 bp):
TAACCTAATTTAATTAAAAACCC
Found at i:42424572 original size:51 final size:49
Alignment explanation
Indices: 42424468--42424593 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 49
42424458 NNNNNNNCCT
42424468 TAACCTAATTTAATTAAAAACCCTAACCTAATTGAACCTAAAACCCAAACC
1 TAACCTAATTTAATTAAAAACCCTAACCTAATTGAACCTAAAA--CAAACC
* **
42424519 TAACTTAATTTAATTAAAAACCCTAACCTAACTT-AATTTAATTAA-AAACCC
1 TAACCTAATTTAATTAAAAACCCTAACCTAA-TTGAACCTAA--AACAAA-CC
*
42424570 TAACCTAATTGAATTAAAAACCCT
1 TAACCTAATTTAATTAAAAACCCT
42424594 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
50 3 0.05
51 59 0.89
52 2 0.03
53 2 0.03
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.29
Consensus pattern (49 bp):
TAACCTAATTTAATTAAAAACCCTAACCTAATTGAACCTAAAACAAACC
Found at i:42424584 original size:28 final size:28
Alignment explanation
Indices: 42424468--42424577 Score: 140
Period size: 28 Copynumber: 4.1 Consensus size: 28
42424458 NNNNNNNCCT
*
42424468 TAACCTAATTTAATTAAAAACCCTAACC
1 TAACTTAATTTAATTAAAAACCCTAACC
* ** *
42424496 TAA-TTGA---ACCT-AAAACCCAAACC
1 TAACTTAATTTAATTAAAAACCCTAACC
42424519 TAACTTAATTTAATTAAAAACCCTAACC
1 TAACTTAATTTAATTAAAAACCCTAACC
42424547 TAACTTAATTTAATTAAAAACCCTAACC
1 TAACTTAATTTAATTAAAAACCCTAACC
42424575 TAA
1 TAA
42424578 TTGAATTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
23 14 0.21
24 5 0.07
27 4 0.06
28 45 0.66
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (28 bp):
TAACTTAATTTAATTAAAAACCCTAACC
Found at i:42432838 original size:27 final size:27
Alignment explanation
Indices: 42432804--42432892 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
42432794 TCCTTAAATA
* * *
42432804 GCCACAAAGGCTTCTATCTCATAGATT
1 GCCACAAAGACTTCCATTTCATAGATT
* *
42432831 GCCACAAAAACTTCCATTTTATAGATT
1 GCCACAAAGACTTCCATTTCATAGATT
* *
42432858 GCCATAAAGACTTCCATTTCATAAATT
1 GCCACAAAGACTTCCATTTCATAGATT
*
42432885 GTCACAAA
1 GCCACAAA
42432893 AGGCTTCTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (27 bp):
GCCACAAAGACTTCCATTTCATAGATT
Found at i:42434630 original size:41 final size:41
Alignment explanation
Indices: 42434597--42434742 Score: 229
Period size: 41 Copynumber: 3.6 Consensus size: 41
42434587 CCGACTTTTG
* **
42434597 GCCTGCTAGACTTAAAGTCCAAAATGTTTCACCGGCATCAA
1 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
42434638 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
1 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
* *
42434679 GCCTGCTAGACATAAAGTCTGAATTGTTTCACCGGCATCTA
1 GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
* *
42434720 GCCTACTAGACATAGAGTCTGAA
1 GCCTGCTAGACATAAAGTCTGAA
42434743 TTATCTCACT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
GCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCAA
Found at i:42434763 original size:82 final size:82
Alignment explanation
Indices: 42434597--42434769 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
42434587 CCGACTTTTG
* *
42434597 GCCTGCTAGACTTAAAGTCCAAAATGTTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAA
1 GCCTGCTAGACATAAAGTCCAAAATGTTTCACCGGCATCAAGCCTACTAGACATAAAGTCTGAAA
* *
42434662 TGTTTCACCGGCATCAA
66 TATCTCACCGGCATCAA
** * * * *
42434679 GCCTGCTAGACATAAAGTCTGAATTGTTTCACCGGCATCTAGCCTACTAGACATAGAGTCTGAAT
1 GCCTGCTAGACATAAAGTCCAAAATGTTTCACCGGCATCAAGCCTACTAGACATAAAGTCTGAAA
*
42434744 TATCTCACTGGCAAT-AA
66 TATCTCACCGGC-ATCAA
*
42434761 GCCTTCTAG
1 GCCTGCTAG
42434770 GCACTGAGCT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 76 0.97
83 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (82 bp):
GCCTGCTAGACATAAAGTCCAAAATGTTTCACCGGCATCAAGCCTACTAGACATAAAGTCTGAAA
TATCTCACCGGCATCAA
Found at i:42442346 original size:11 final size:11
Alignment explanation
Indices: 42442326--42442354 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42442316 TAAAATATAA
42442326 TTTT-ATATTT
1 TTTTAATATTT
42442336 TTTTAATATTT
1 TTTTAATATTT
42442347 TTTTAATA
1 TTTTAATA
42442355 AAATACGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTAATATTT
Found at i:42442500 original size:18 final size:18
Alignment explanation
Indices: 42442477--42442522 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
42442467 ATTTAAATTG
42442477 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
*
42442495 CGGTCGC-GTTGC-TTTT
1 CGGTCGCGGTCGCGTTTT
42442511 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
42442523 GACATAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 4 0.17
17 4 0.17
18 7 0.29
ACGTcount: A:0.00, C:0.28, G:0.39, T:0.33
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:42450890 original size:22 final size:22
Alignment explanation
Indices: 42450862--42450904 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42450852 ATACCTAATT
**
42450862 TTTTCTTTTTTTTCCTTCCTTC
1 TTTTCTTTTCCTTCCTTCCTTC
42450884 TTTTCTTTTCCTTCCTTCCTT
1 TTTTCTTTTCCTTCCTTCCTT
42450905 ATTATTTCTT
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:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCTTTTCCTTCCTTCCTTC
Found at i:42450894 original size:18 final size:17
Alignment explanation
Indices: 42450864--42450901 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
42450854 ACCTAATTTT
42450864 TTCTTTTTTTTCCTTCC
1 TTCTTTTTTTTCCTTCC
42450881 TTCTTTTCTTTTCCTTCC
1 TTCTTTT-TTTTCCTTCC
42450899 TTC
1 TTC
42450902 CTTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTCTTTTTTTTCCTTCC
Found at i:42451011 original size:27 final size:27
Alignment explanation
Indices: 42450973--42451075 Score: 145
Period size: 27 Copynumber: 3.8 Consensus size: 27
42450963 AAAATAACAG
* *
42450973 CATTGGCGCCTCTCA-GAATGGCACCAC
1 CATTGGCGCCTCCCAGGTA-GGCACCAC
42451000 CATTGGCGCCTCCCAGGTAGGCACCAC
1 CATTGGCGCCTCCCAGGTAGGCACCAC
**
42451027 CATTGGCGCCTCTTAGGTAGGCACCAC
1 CATTGGCGCCTCCCAGGTAGGCACCAC
*
42451054 CATTGGCGCCTCCCAGATAGGC
1 CATTGGCGCCTCCCAGGTAGGC
42451076 GCCAATACTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 66 0.97
28 2 0.03
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.18
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGGTAGGCACCAC
Found at i:42451037 original size:54 final size:54
Alignment explanation
Indices: 42450973--42451075 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
42450963 AAAATAACAG
*
42450973 CATTGGCGCCTCTCAGA-ATGGCACCACCATTGGCGCCTCCCAGGTAGGCACCAC
1 CATTGGCGCCTCTCAGATA-GGCACCACCATTGGCGCCTCCCAGATAGGCACCAC
* *
42451027 CATTGGCGCCTCTTAGGTAGGCACCACCATTGGCGCCTCCCAGATAGGC
1 CATTGGCGCCTCTCAGATAGGCACCACCATTGGCGCCTCCCAGATAGGC
42451076 GCCAATACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 44 0.98
55 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.18
Consensus pattern (54 bp):
CATTGGCGCCTCTCAGATAGGCACCACCATTGGCGCCTCCCAGATAGGCACCAC
Found at i:42456029 original size:3 final size:3
Alignment explanation
Indices: 42456016--42456061 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
42456006 AGCTATTTCC
*
42456016 ATT ATTT ATT ATT A-T ATT ATTT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
42456062 TCTATATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42456036 original size:15 final size:15
Alignment explanation
Indices: 42456016--42456060 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
42456006 AGCTATTTCC
42456016 ATTATTTATTATTAT
1 ATTATTTATTATTAT
*
42456031 ATTATTTATTATCATT
1 ATTATTTATTATTA-T
42456047 ATTA-TTATTATTAT
1 ATTATTTATTATTAT
42456061 TTCTATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 21 0.78
16 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTATTTATTATTAT
Found at i:42456119 original size:22 final size:23
Alignment explanation
Indices: 42456087--42456151 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
42456077 ACGCATTGTT
*
42456087 TTTTTTATATAATATATATATGCA
1 TTTTTT-TATAATATATATACGCA
*
42456111 -TTTTTTAT-ATAGTATACACGCA
1 TTTTTTTATAATA-TATATACGCA
42456133 TTATTTTTATAATATATAT
1 TT-TTTTTATAATATATAT
42456152 GTATATATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 11 0.32
23 6 0.18
24 11 0.32
25 3 0.09
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (23 bp):
TTTTTTTATAATATATATACGCA
Found at i:42456119 original size:24 final size:24
Alignment explanation
Indices: 42456087--42456151 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
42456077 ACGCATTGTT
*
42456087 TTTTTTATATAATATATATATGCA
1 TTTTTTATATAATATATATACGCA
* *
42456111 TTTTTTATAT-A-GTATACACGCA
1 TTTTTTATATAATATATATACGCA
42456133 TTATTTT-TATAATATATAT
1 TT-TTTTATATAATATATAT
42456152 GTATATATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 13 0.39
23 6 0.18
24 14 0.42
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (24 bp):
TTTTTTATATAATATATATACGCA
Found at i:42456164 original size:30 final size:28
Alignment explanation
Indices: 42456116--42456187 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 28
42456106 ATGCATTTTT
42456116 TATATAGTATACACGCATTAT-TTTTATAA
1 TATATAGTATACACGCATT-TCTTTTAT-A
* *
42456145 TATATATGTATATATGCATTTCTTTTATA
1 TATATA-GTATACACGCATTTCTTTTATA
42456174 TAGTATACGTATAC
1 TA-TATA-GTATAC
42456188 CTGTATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (28 bp):
TATATAGTATACACGCATTTCTTTTATA
Found at i:42456178 original size:54 final size:51
Alignment explanation
Indices: 42456075--42456181 Score: 151
Period size: 51 Copynumber: 2.0 Consensus size: 51
42456065 ATATTCATAC
* * *
42456075 ACACGCATTGTTTTTTTTATATAATATATATATGCATTTTTTATATAGTAT
1 ACACGCATTATTTTTATAATATAATATATATATGCATTTTTTATATAGTAT
*
42456126 ACACGCATTATTTTTATAATATATATGTATATATGCATTTCTTTTATATAGTAT
1 ACACGCATTATTTTTATAATATA-ATATATATATGCA-TT-TTTTATATAGTAT
42456180 AC
1 AC
42456182 GTATACCTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 20 0.41
52 12 0.24
53 2 0.04
54 15 0.31
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.50
Consensus pattern (51 bp):
ACACGCATTATTTTTATAATATAATATATATATGCATTTTTTATATAGTAT
Found at i:42457661 original size:3 final size:3
Alignment explanation
Indices: 42457653--42457678 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42457643 GATTTTGTCC
42457653 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
42457679 CCTACTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:42461688 original size:41 final size:41
Alignment explanation
Indices: 42461636--42461731 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
42461626 GATCCTGTCT
*
42461636 CATCATGAACATGGTTGCTTCAACTTTGCATTGTCTTCTCA
1 CATCATGAACATGGTTGCTTCAACGTTGCATTGTCTTCTCA
* *
42461677 CATCATGAACATGGTTGCTTCCACGTTGCATTGTCTTGTCA
1 CATCATGAACATGGTTGCTTCAACGTTGCATTGTCTTCTCA
42461718 CATCATGAACATGG
1 CATCATGAACATGG
42461732 GCATTGTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (41 bp):
CATCATGAACATGGTTGCTTCAACGTTGCATTGTCTTCTCA
Found at i:42470856 original size:5 final size:5
Alignment explanation
Indices: 42470846--42470870 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42470836 CATAATTATG
42470846 AGCTA AGCTA AGCTA AGCTA AGCTA
1 AGCTA AGCTA AGCTA AGCTA AGCTA
42470871 GCTCATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
AGCTA
Found at i:42477497 original size:246 final size:247
Alignment explanation
Indices: 42477042--42477533 Score: 842
Period size: 246 Copynumber: 2.0 Consensus size: 247
42477032 TTGTTAACTA
*
42477042 AGGAGGGACATAAATTATACATAAGCCCAAAATGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
1 AGGAGGGACATAAATTATACATAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
* * * *
42477107 TCAGGAGAATTGGTGAAATAATGGCAAAATGGGAAAATAACAAAATTTACTAAAATAAAAATGAG
66 TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
**
42477172 ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAATGTCCTA
131 ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAACATCCTA
*
42477237 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTTAAATG
196 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAATG
* *
42477289 AGGAGGGACATAAATTGTA-TTAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
1 AGGAGGGACATAAATTATACATAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
42477353 TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
66 TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
* * * * *
42477418 ACTAAATTATAATATCTGGAATTCTCTTCATATTTTGTTCATTATCATCAGCCAAAAACATCCTA
131 ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAACATCCTA
42477483 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAAT
196 AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAAT
42477534 ACGAAGCTAG
Statistics
Matches: 230, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
246 212 0.92
247 18 0.08
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (247 bp):
AGGAGGGACATAAATTATACATAAGCCCAAAAGGAGATATTTTGGGTGGCATAAGCTGAGAAAAA
TCAGGAGAATTGATGAAATAAGGGAAAAATAGGAAAATAACAAAATTTACTAAAATAAAAATGAG
ACCAAATTAGAATATCTAGAATTATCTTCATATTTTGTTCATTATCATCAACCAAAAACATCCTA
AGGGTTTATTCAAGCTGGTATTTCATAATTTTTGCACCAAAAAATTCAAATG
Found at i:42477640 original size:21 final size:20
Alignment explanation
Indices: 42477614--42477677 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
42477604 GTTCATGTAA
42477614 CTTGAATTATATTCTTAAATG
1 CTTGAA-TATATTCTTAAATG
* *
42477635 CTTGAAGTATATT-TTTATTG
1 CTTGAA-TATATTCTTAAATG
*
42477655 ATGTGAATATATTCTTAAATG
1 CT-TGAATATATTCTTAAATG
42477676 CT
1 CT
42477678 CAACCCGAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 12 0.35
21 22 0.65
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (20 bp):
CTTGAATATATTCTTAAATG
Found at i:42494287 original size:20 final size:21
Alignment explanation
Indices: 42494248--42494287 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
42494238 CACCAAGTGA
42494248 AAACATTTACATGAACAACTTC
1 AAACATTTACAT-AACAACTTC
*
42494270 AAACATTTATAT-ACAACT
1 AAACATTTACATAACAACT
42494288 ATGTGTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (21 bp):
AAACATTTACATAACAACTTC
Found at i:42494825 original size:35 final size:36
Alignment explanation
Indices: 42494779--42494943 Score: 173
Period size: 34 Copynumber: 4.8 Consensus size: 36
42494769 TAAAGAGTGT
42494779 GCCCAACACTAGTCAGATAAACTGACAGA-AGTTAC
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
* * **
42494814 GCCCAACACTAGTCAGA-GAACCGA-AGATAGTTGT
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
* *
42494848 GCCCAGCACTAGTCAGATAAACTAACAGA-AGTTAC
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
* * * * *
42494883 GCCCAGCACTAGTCGGAT-AACCGAC-GATAATTAT
1 GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
42494917 GCCCAGA-ACTAGTCAGATAAACTGACA
1 GCCCA-ACACTAGTCAGATAAACTGACA
42494944 AAATTGCGCC
Statistics
Matches: 105, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
33 5 0.05
34 49 0.47
35 48 0.46
36 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (36 bp):
GCCCAACACTAGTCAGATAAACTGACAGATAGTTAC
Found at i:42494887 original size:69 final size:69
Alignment explanation
Indices: 42494776--42494998 Score: 288
Period size: 69 Copynumber: 3.2 Consensus size: 69
42494766 ATATAAAGAG
* * * *
42494776 TGTGCCCAACACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCAGAGAACCGAAGA
1 TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCGGATAACCGACGA
42494841 TAGT
66 TAGT
* *
42494845 TGTGCCCAGCACTAGTCAGATAAACTAACAGAAGTTACGCCCAGCACTAGTCGGATAACCGACGA
1 TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCGGATAACCGACGA
*
42494910 TAAT
66 TAGT
* * * * * * *
42494914 TATGCCCAGAACTAGTCAGATAAACTGACA-AAATTGCG-CCAAGCGCTAGTTGGATAACCGGCG
1 TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAA-CACTAGTCGGATAACCGACG
*
42494977 ATGGT
65 ATAGT
42494982 TGTGCCCAGCACTAGTC
1 TGTGCCCAGCACTAGTC
42494999 GAATGAATCA
Statistics
Matches: 133, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 3 0.02
68 41 0.31
69 89 0.67
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (69 bp):
TGTGCCCAGCACTAGTCAGATAAACTGACAGAAGTTACGCCCAACACTAGTCGGATAACCGACGA
TAGT
Found at i:42498136 original size:18 final size:18
Alignment explanation
Indices: 42498096--42498136 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
42498086 TTAATCTTTG
42498096 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
42498113 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
42498132 -TTTAT
1 ATTTAT
42498137 CTGACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:42503505 original size:42 final size:42
Alignment explanation
Indices: 42503429--42503515 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
42503419 CTAGAAGCAC
* * ** *
42503429 TTTCTTGCAACGTATGCTGAAAACATGTCTAGCTTAATGCAT
1 TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAATGCAT
* *
42503471 TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAGTGCGT
1 TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAATGCAT
42503513 TTT
1 TTT
42503516 AAAAAATCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTCTTGCAAAGTACGCTGAAAACACATCCAGCTTAATGCAT
Found at i:42509510 original size:15 final size:16
Alignment explanation
Indices: 42509485--42509526 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42509475 TAAACTAAAA
42509485 CAAAGGAGAAATGAA-G
1 CAAA-GAGAAATGAATG
*
42509501 CAAAGAGAAACGAATG
1 CAAAGAGAAATGAATG
42509517 CAAAGA-AAAT
1 CAAAGAGAAAT
42509527 TGATCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.60, C:0.10, G:0.24, T:0.07
Consensus pattern (16 bp):
CAAAGAGAAATGAATG
Found at i:42525490 original size:20 final size:19
Alignment explanation
Indices: 42525465--42525509 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
42525455 AATAAACACC
42525465 AAAAAAA-ATTTTAGAAAATT
1 AAAAAAAGATTTTA-AAAA-T
42525485 AAAAAAAGTATTTTAAAAAT
1 AAAAAAAG-ATTTTAAAAAT
42525505 AAAAA
1 AAAAA
42525510 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAAAAGATTTTAAAAAT
Found at i:42525491 original size:21 final size:20
Alignment explanation
Indices: 42525465--42525509 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
42525455 AATAAACACC
42525465 AAAAAA-AATTTTAGAAAATTA
1 AAAAAAGAATTTTA-AAAA-TA
*
42525486 AAAAAAGTATTTTAAAAATA
1 AAAAAAGAATTTTAAAAATA
42525506 AAAA
1 AAAA
42525510 GTATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 10 0.45
22 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAAAAGAATTTTAAAAATA
Found at i:42543169 original size:25 final size:25
Alignment explanation
Indices: 42543135--42543183 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
42543125 TTTAATTAAT
*
42543135 ACAAGACTTTGGACTGTTCTAAGAC
1 ACAAGACTTTGGACTGTTCCAAGAC
*
42543160 ACAAGACTTTGGATTGTTCCAAGA
1 ACAAGACTTTGGACTGTTCCAAGA
42543184 TGGTCTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (25 bp):
ACAAGACTTTGGACTGTTCCAAGAC
Found at i:42558696 original size:42 final size:41
Alignment explanation
Indices: 42558650--42558760 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 41
42558640 GCACATAAGT
* * * *
42558650 GCTAAACGGAAACCCATGAGGGTTGAACAGAAGCTTATAGGA
1 GCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAGA-GA
* * *
42558692 GCTAAACAGAAACCCAAAAGGGTTAAACTGAAGCTCAGAGA
1 GCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAGAGA
* * * *
42558733 GCTGAACGGAAACTCATTAGGGATAAAC
1 GCTAAACGGAAACCCATAAGGGTTAAAC
42558761 TAAAACTCAT
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 24 0.43
42 32 0.57
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.15
Consensus pattern (41 bp):
GCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTCAGAGA
Found at i:42560743 original size:106 final size:107
Alignment explanation
Indices: 42560531--42560744 Score: 421
Period size: 106 Copynumber: 2.0 Consensus size: 107
42560521 TTAATTAATT
42560531 AACTGTTTGAACTAACTAATGATATTATAAAAATATAAAAAAAATTATGTTAGAAATTAAAATTT
1 AACTGTTTGAACTAACTAATGATATTATAAAAATATAAAAAAAATTATGTTAGAAATTAAAATTT
42560596 TAATGTTTTCAACAAAAGTAAAAAGGAAAAAGAACCATGTGG
66 TAATGTTTTCAACAAAAGTAAAAAGGAAAAAGAACCATGTGG
42560638 AACTGTTTGAA-TAACTAATGATATTATAAAAATATAAAAAAAATTATGTTAGAAATTAAAATTT
1 AACTGTTTGAACTAACTAATGATATTATAAAAATATAAAAAAAATTATGTTAGAAATTAAAATTT
42560702 TAATGTTTTCAACAAAAGTAAAAAGGAAAAAGAACCATGTGG
66 TAATGTTTTCAACAAAAGTAAAAAGGAAAAAGAACCATGTGG
42560744 A
1 A
42560745 TAGACCCACG
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 96 0.90
107 11 0.10
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (107 bp):
AACTGTTTGAACTAACTAATGATATTATAAAAATATAAAAAAAATTATGTTAGAAATTAAAATTT
TAATGTTTTCAACAAAAGTAAAAAGGAAAAAGAACCATGTGG
Found at i:42562102 original size:16 final size:16
Alignment explanation
Indices: 42562081--42562145 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
42562071 CGCTGTATTG
42562081 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
*
42562097 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATA
*
42562113 GAATAGAGGTGTAAT-
1 GAATAGAGGCGTAATA
*
42562128 GAAATAGAGGTGTAATA
1 G-AATAGAGGCGTAATA
42562145 G
1 G
42562146 CAAATCAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
15 1 0.02
16 43 0.96
17 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.34, T:0.22
Consensus pattern (16 bp):
GAATAGAGGCGTAATA
Found at i:42562120 original size:32 final size:32
Alignment explanation
Indices: 42562079--42562143 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
42562069 TTCGCTGTAT
42562079 TGGAATAGAGGCGTAAT-AGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAATGA-AATAGAGGCGTAA
* *
42562111 TGGAATAGAGGTGTAATGAAATAGAGGTGTAA
1 TGGAATAGAGGCGTAATGAAATAGAGGCGTAA
42562143 T
1 T
42562144 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.23
Consensus pattern (32 bp):
TGGAATAGAGGCGTAATGAAATAGAGGCGTAA
Found at i:42562801 original size:47 final size:47
Alignment explanation
Indices: 42562748--42562887 Score: 148
Period size: 47 Copynumber: 3.0 Consensus size: 47
42562738 TTAATAATGA
*
42562748 TATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
** * * *
42562795 TATATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATGA
1 TATATAATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATGAAT-T
*
42562839 TATATAATTTCATAAAATTCTTAATAATAAATATTCTTATATGAATT
1 TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
42562886 TA
1 TA
42562888 CTAAAATCAT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
43 3 0.04
44 25 0.35
45 7 0.10
46 6 0.08
47 28 0.39
48 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (47 bp):
TATATAATTTCATAAAATTCTTAATAATAAATTTTCTTATATGAATT
Found at i:42562843 original size:44 final size:44
Alignment explanation
Indices: 42562725--42562848 Score: 119
Period size: 44 Copynumber: 2.8 Consensus size: 44
42562715 NNNNNNNNNN
** *
42562725 TATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGA
1 TATTAAATATAATTTAATAATGATATATAA-TT--TAAAATAATTAA
* * *
42562772 TAATAAAT-T-TTCTTATATGAAT-TTATATAATTTAAAATAATTAA
1 TATTAAATATAAT-TTA-AT-AATGATATATAATTTAAAATAATTAA
42562816 TATTAAATATAATTTAATAATGATATATAATTT
1 TATTAAATATAATTTAATAATGATATATAATTT
42562849 CATAAAATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
43 3 0.05
44 28 0.45
45 5 0.08
46 7 0.11
47 16 0.26
48 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (44 bp):
TATTAAATATAATTTAATAATGATATATAATTTAAAATAATTAA
Found at i:42563122 original size:24 final size:24
Alignment explanation
Indices: 42563087--42563136 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
42563077 GATAAAGTAT
*
42563087 TTATCACCTCAAATGTGATTTGGG
1 TTATCACATCAAATGTGATTTGGG
42563111 TTATCACATCAAATGTGATTTGGG
1 TTATCACATCAAATGTGATTTGGG
42563135 TT
1 TT
42563137 CAAATTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TTATCACATCAAATGTGATTTGGG
Found at i:42574476 original size:5 final size:5
Alignment explanation
Indices: 42574436--42574461 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42574426 GCAAATCGGC
42574436 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
42574462 TCGGATGAAA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:42576417 original size:30 final size:30
Alignment explanation
Indices: 42576381--42576437 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42576371 TTTTACATAT
42576381 ATATTTTGAATTTTTATAAAAT-TTTTATTC
1 ATATTTTGAATTTTTA-AAAATATTTTATTC
*
42576411 ATATTTTTAATTTTTAAAAATATTTTA
1 ATATTTTGAATTTTTAAAAATATTTTA
42576438 ACGTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
ATATTTTGAATTTTTAAAAATATTTTATTC
Found at i:42576493 original size:22 final size:20
Alignment explanation
Indices: 42576451--42576497 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
42576441 TGAATTTCAA
*
42576451 TATTTTTAATAATTTATATT
1 TATTTTTAATAATTTAAATT
42576471 TATTTTTAATATATTTTAAATT
1 TATTTTTAATA-A-TTTAAATT
42576493 T-TTTT
1 TATTTT
42576498 AAAAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 5 0.21
22 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTAATAATTTAAATT
Found at i:42587161 original size:21 final size:21
Alignment explanation
Indices: 42587137--42587193 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
42587127 ATTGGGTGGA
* *
42587137 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTAT
42587158 TCAGCTCTTACGAGCTTCTAT
1 TCAGCTCTTACGAGCTTCTAT
*
42587179 TCAACT-TT-CGAGCTT
1 TCAGCTCTTACGAGCTT
42587194 TTGTTGGCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 7 0.21
20 2 0.06
21 24 0.73
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTAT
Found at i:42598403 original size:31 final size:31
Alignment explanation
Indices: 42598364--42598432 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
42598354 TATGTCGCAG
42598364 TTAA-TCTATTTCTAAATTGTGCCAATCAAT
1 TTAATTCTATTTCTAAATTGTGCCAATCAAT
42598394 TTAATTCTATTTCTAAATTGTGCCAATCAAT
1 TTAATTCTATTTCTAAATTGTGCCAATCAAT
42598425 TTAATTCT
1 TTAATTCT
42598433 TCATAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAATTCTATTTCTAAATTGTGCCAATCAAT
Found at i:42599389 original size:23 final size:23
Alignment explanation
Indices: 42599357--42599400 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
42599347 AATACCATTT
42599357 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
42599380 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
42599401 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:42599393 original size:13 final size:11
Alignment explanation
Indices: 42599361--42599403 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
42599351 CCATTTTCTA
*
42599361 AATAAAATAAT
1 AATAAAATATT
42599372 AAT-AAATATCT
1 AATAAAATAT-T
42599383 AAGTAAAATATT
1 AA-TAAAATATT
42599395 AATAAAATA
1 AATAAAATA
42599404 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:42603163 original size:30 final size:30
Alignment explanation
Indices: 42603056--42603165 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
42603046 GTTTTGTTAT
* * ** *
42603056 TTATATATATAATATATATGGGTTTTGCTG
1 TTATATGTATAATATATTTGGGTCATGGTG
* **
42603086 TTATA--TATAATATATGTACGTGCATGGGTG
1 TTATATGTATAATATATTTGGGT-CAT-GGTG
*
42603116 TTATATGAATAATATATTTGGGTCATGGTG
1 TTATATGTATAATATATTTGGGTCATGGTG
42603146 TTATATGTATAATATATTTG
1 TTATATGTATAATATATTTG
42603166 CGTGGGTCAG
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
28 13 0.20
29 1 0.02
30 36 0.55
31 3 0.05
32 12 0.18
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (30 bp):
TTATATGTATAATATATTTGGGTCATGGTG
Found at i:42611288 original size:17 final size:19
Alignment explanation
Indices: 42611263--42611299 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
42611253 AATTCAAAGT
*
42611263 ATATTCAATT-AA-CACAA
1 ATATACAATTCAATCACAA
42611280 ATATACAATTCAATCACAA
1 ATATACAATTCAATCACAA
42611299 A
1 A
42611300 CATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (19 bp):
ATATACAATTCAATCACAA
Found at i:42631643 original size:29 final size:31
Alignment explanation
Indices: 42631590--42631649 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
42631580 AACCTCTTCG
42631590 CTTTCCTCTCAAAACTTTTACT-CCCTCCCA
1 CTTTCCTCTCAAAACTTTTACTCCCCTCCCA
* **
42631620 CTTTCC-CTCATAACTTTTGTTCCCCTCCCA
1 CTTTCCTCTCAAAACTTTTACTCCCCTCCCA
42631650 TCCTACCCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.17, C:0.43, G:0.02, T:0.38
Consensus pattern (31 bp):
CTTTCCTCTCAAAACTTTTACTCCCCTCCCA
Found at i:42638632 original size:69 final size:68
Alignment explanation
Indices: 42638549--42638683 Score: 234
Period size: 69 Copynumber: 2.0 Consensus size: 68
42638539 CGTTGAGCGC
* *
42638549 ACATAAAAAAATCTAACACTCGTCATCATTATCAAATTATTGTGAAATGCAAATGTGAGTTATGG
1 ACATAAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGCAAATGTCAGTTATGG
42638614 CGG
66 CGG
*
42638617 ACATAAAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGTAAATGTCAGTTATG
1 ACAT-AAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGCAAATGTCAGTTATG
42638682 GC
65 GC
42638684 AGTTGTATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 4 0.06
69 59 0.94
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (68 bp):
ACATAAAAAAATCTAACACTCATCATCATTATCAAATTATTGTGAAATGCAAATGTCAGTTATGG
CGG
Found at i:42639190 original size:9 final size:9
Alignment explanation
Indices: 42639176--42639261 Score: 111
Period size: 9 Copynumber: 9.4 Consensus size: 9
42639166 TTTGGTTAAA
42639176 AATTACCCG
1 AATTACCCG
42639185 AATTACCCG
1 AATTACCCG
42639194 AATTACCCG
1 AATTACCCG
*
42639203 AATTAGCCG
1 AATTACCCG
*
42639212 AATTAACCG
1 AATTACCCG
*
42639221 AATTAACCG
1 AATTACCCG
42639230 AATTA-CCG
1 AATTACCCG
*
42639238 AAAAATACCCG
1 --AATTACCCG
42639249 AATTACCCG
1 AATTACCCG
42639258 AATT
1 AATT
42639262 TTTTTTATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
8 3 0.04
9 60 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:42642649 original size:32 final size:32
Alignment explanation
Indices: 42642588--42642650 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
42642578 TGCATGAGCT
*
42642588 ACACGGGTTGAACCATTACATACGACCAGACC
1 ACACGGGTTGAACCATTACACACGACCAGACC
* * * *
42642620 ACACTGGTTGAACCATTTCACATGGCCAGAC
1 ACACGGGTTGAACCATTACACACGACCAGAC
42642651 AACATAGCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (32 bp):
ACACGGGTTGAACCATTACACACGACCAGACC
Found at i:42645067 original size:30 final size:29
Alignment explanation
Indices: 42645013--42645072 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
42645003 CGAGCCTTGG
42645013 GGCAAAAATGTAATTATGTAAAAGTTTAGA
1 GGCAAAAATGTAATTATGTAAAAG-TTAGA
* *
42645043 GGCAAAATTGTAATTTTG-ACAAAGTTAGA
1 GGCAAAAATGTAATTATGTA-AAAGTTAGA
42645072 G
1 G
42645073 TCGAGGGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (29 bp):
GGCAAAAATGTAATTATGTAAAAGTTAGA
Found at i:42645269 original size:50 final size:50
Alignment explanation
Indices: 42645194--42645513 Score: 390
Period size: 50 Copynumber: 6.4 Consensus size: 50
42645184 GTTGGTGAAT
42645194 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* * *
42645244 TGGGATATGGCGTTGGTACCGAGATGAGAGGTCCCATGTAAGACCATATC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* **
42645294 TGAGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
* * * * **
42645344 TGGGACATGGCATGGGCACCGATATAAGAACATCCCATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTC
* *
42645395 TGGGACATGGTGTTGGCACCGAGATGAGAGGTCCC-TCGTAAAACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCAT-GTAAGACCATGTC
* * * * * **
42645445 TGGGGCATGGCATGGGCACCGATATAAGAACATCCCATGTAAGACCATGTC
1 TGGGACATGGCGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTC
* * *
42645496 TGAGACATAGCTTTGGCA
1 TGGGACATGGCGTTGGCA
42645514 TGTTATGATC
Statistics
Matches: 226, Mismatches: 40, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
49 1 0.00
50 153 0.68
51 71 0.31
52 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
Found at i:42645428 original size:101 final size:101
Alignment explanation
Indices: 42645197--42645513 Score: 465
Period size: 101 Copynumber: 3.1 Consensus size: 101
42645187 GGTGAATTGG
* * * * *
42645197 GACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGTA
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
* * ** *
42645262 CCGAGATGAG-AGGTCCCATGTAAGACCATATCTGA
66 CCGATATAAGAACATCCCATGTAAGACCATGTCTGA
*
42645297 GACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCA
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
*
42645362 CCGATATAAGAACATCCCATGTAAGACCATGTCTGG
66 CCGATATAAGAACATCCCATGTAAGACCATGTCTGA
* * * *
42645398 GACATGGTGTTGGCACCGAGATGAGAGGTCCCTCGTAAAACCATGTCTGGGGCATGGCATGGGCA
1 GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
42645463 CCGATATAAGAACATCCCATGTAAGACCATGTCTGA
66 CCGATATAAGAACATCCCATGTAAGACCATGTCTGA
* *
42645499 GACATAGCTTTGGCA
1 GACATGGCGTTGGCA
42645514 TGTTATGATC
Statistics
Matches: 196, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
100 67 0.34
101 129 0.66
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (101 bp):
GACATGGCGTTGGCACCGAGATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
CCGATATAAGAACATCCCATGTAAGACCATGTCTGA
Found at i:42649021 original size:9 final size:9
Alignment explanation
Indices: 42649009--42649037 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
42648999 TGACGGAAAT
42649009 GGTGGTGGA
1 GGTGGTGGA
42649018 GGTGGTGGA
1 GGTGGTGGA
42649027 GGTGGTGGA
1 GGTGGTGGA
42649036 GG
1 GG
42649038 CAGTGGGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.69, T:0.21
Consensus pattern (9 bp):
GGTGGTGGA
Found at i:42649043 original size:18 final size:18
Alignment explanation
Indices: 42649009--42649043 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42648999 TGACGGAAAT
**
42649009 GGTGGTGGAGGTGGTGGA
1 GGTGGTGGAGGCAGTGGA
42649027 GGTGGTGGAGGCAGTGG
1 GGTGGTGGAGGCAGTGG
42649044 GGGAGGAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.03, G:0.66, T:0.20
Consensus pattern (18 bp):
GGTGGTGGAGGCAGTGGA
Found at i:42650507 original size:24 final size:24
Alignment explanation
Indices: 42650440--42650507 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
42650430 TGGAGGAACA
42650440 ATAATACTTCCATTGAAAATATCC
1 ATAATACTTCCATTGAAAATATCC
*
42650464 ---ATA-TT--ATTGAGAAACA-CC
1 ATAATACTTCCATTGA-AAATATCC
42650482 ATAATACTTCCATTGAAAATATCC
1 ATAATACTTCCATTGAAAATATCC
42650506 AT
1 AT
42650508 GTTATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 2 0.06
21 6 0.18
22 2 0.06
23 4 0.12
24 9 0.26
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (24 bp):
ATAATACTTCCATTGAAAATATCC
Found at i:42656940 original size:51 final size:51
Alignment explanation
Indices: 42656881--42656981 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
42656871 CAAGACTTAG
42656881 TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAAA
1 TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAAA
*
42656932 TCAATTATCTCGCAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAA
1 TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAA
42656982 CTCTTATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (51 bp):
TCAATTATCTCGAAATGCAAGTAACATAAACCTCTTTAGACCTAGTCAAAA
Found at i:42661027 original size:25 final size:25
Alignment explanation
Indices: 42660999--42661064 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
42660989 CTCGCTTGAA
*
42660999 CTTCCCGATATATGGCTATCCGGAG
1 CTTCCCGATATATGGCTATACGGAG
* * *
42661024 CTTCCTGATAAATGGCTCTACGGAG
1 CTTCCCGATATATGGCTATACGGAG
* *
42661049 CTACCCGTTAT-TGGCT
1 CTTCCCGATATATGGCT
42661065 TGCATGAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 5 0.15
25 28 0.85
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (25 bp):
CTTCCCGATATATGGCTATACGGAG
Found at i:42661139 original size:25 final size:25
Alignment explanation
Indices: 42661081--42661163 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
42661071 AGCTTCTTGA
* *
42661081 ATATGGCTCTGATGAGCTTCCCCTT
1 ATATGGCTCGGATAAGCTTCCCCTT
**
42661106 ATACAGCTCGGATAAGCTTCCCCTT
1 ATATGGCTCGGATAAGCTTCCCCTT
* *
42661131 ATATGGCTCGAGAGAGAGCTTCCCGTTT
1 ATATGGCTCG-GATA-AGCTTCCC-CTT
42661159 ATATG
1 ATATG
42661164 CTCATATGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 29 0.62
26 3 0.06
27 8 0.17
28 7 0.15
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (25 bp):
ATATGGCTCGGATAAGCTTCCCCTT
Found at i:42663220 original size:25 final size:25
Alignment explanation
Indices: 42663142--42663302 Score: 98
Period size: 25 Copynumber: 6.4 Consensus size: 25
42663132 AATTCATATT
* *
42663142 CGGGAATGCTTATATGAGCACATA-AA
1 CGGGAA-GCTCATCTGAGC-CATATAA
* *
42663168 CAGGAAGCTCTCTCTCGAGCCATATAA
1 CGGGAAGCTC-ATCT-GAGCCATATAA
* *
42663195 CGGGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATCTGAGCCATATAA
* * *
42663220 CGGGAAGCTTATCTGAGCAATATGA
1 CGGGAAGCTCATCTGAGCCATATAA
** ** * *
42663245 CAAGAAGCTCATAAGAGCTATATTTA
1 CGGGAAGCTCATCTGAGCCATA-TAA
42663271 --GGAAGCTCATGC-GAGCCA-ATAA
1 CGGGAAGCTCAT-CTGAGCCATATAA
42663293 CGGGAAGCTC
1 CGGGAAGCTC
42663303 TGAAGAGCCA
Statistics
Matches: 104, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
22 2 0.02
23 1 0.01
24 22 0.21
25 49 0.47
26 15 0.14
27 15 0.14
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (25 bp):
CGGGAAGCTCATCTGAGCCATATAA
Found at i:42663368 original size:23 final size:23
Alignment explanation
Indices: 42663342--42663387 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42663332 TAGTCATATA
* *
42663342 TCGGGAAGTTCAAGCGAGCCATT
1 TCGGGAAGCTCAAGAGAGCCATT
*
42663365 TCGGGAAGCTCCAGAGAGCCATT
1 TCGGGAAGCTCAAGAGAGCCATT
42663388 AATTAGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (23 bp):
TCGGGAAGCTCAAGAGAGCCATT
Found at i:42663415 original size:26 final size:26
Alignment explanation
Indices: 42663368--42663438 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
42663358 AGCCATTTCG
* *
42663368 GGAAGCTC-CAGAGAGCCATTAATTA
1 GGAAGCTCACAAAGAGCCATTAATGA
* *
42663393 GGAAGCTCACAAAGAGCCTTTAATGC
1 GGAAGCTCACAAAGAGCCATTAATGA
*
42663419 GGAAGCTCACGAAGAGCCAT
1 GGAAGCTCACAAAGAGCCAT
42663439 ATATCGGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 8 0.21
26 31 0.79
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATTAATGA
Found at i:42678721 original size:25 final size:26
Alignment explanation
Indices: 42678692--42678749 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
42678682 AAAATATAGG
42678692 GAAAATAGAAAAAATTA-TAAAAATAT
1 GAAAATAGAAAAAATTATTAAAAAT-T
** *
42678718 -AAAATATCAAAATTTATTAAAAATT
1 GAAAATAGAAAAAATTATTAAAAATT
42678743 GAAAATA
1 GAAAATA
42678750 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (26 bp):
GAAAATAGAAAAAATTATTAAAAATT
Found at i:42687411 original size:53 final size:53
Alignment explanation
Indices: 42687354--42687510 Score: 166
Period size: 53 Copynumber: 3.1 Consensus size: 53
42687344 TATTCATGTG
42687354 AATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTA
1 AATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTA
* * * * * ** * * * *
42687407 AATTTTA-GAAACT-TCTT-TT---AAAT-TAATTTTATTTATTATTCATGTG
1 AATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTA
42687453 AATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTA
1 AATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTA
42687506 AATTT
1 AATTT
42687511 TAGAAACTTC
Statistics
Matches: 75, Mismatches: 22, Indels: 14
0.68 0.20 0.13
Matches are distributed among these distances:
46 22 0.29
47 8 0.11
48 3 0.04
49 2 0.03
50 2 0.03
51 3 0.04
52 8 0.11
53 27 0.36
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (53 bp):
AATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTA
Found at i:42687441 original size:99 final size:100
Alignment explanation
Indices: 42687323--42687523 Score: 395
Period size: 99 Copynumber: 2.0 Consensus size: 100
42687313 TATTTTAAAA
42687323 TTTAAATTAATTTTTATTTATTATTCATGTGAATTTGATTAAAATATTTTATTCAAAAATAAAAT
1 TTTAAATTAATTTTTATTTATTATTCATGTGAATTTGATTAAAATATTTTATTCAAAAATAAAAT
42687388 AATATTGATTATTCTTTTAAATTTTAGAAACTTCT
66 AATATTGATTATTCTTTTAAATTTTAGAAACTTCT
42687423 TTTAAATTAA-TTTTATTTATTATTCATGTGAATTTGATTAAAATATTTTATTCAAAAATAAAAT
1 TTTAAATTAATTTTTATTTATTATTCATGTGAATTTGATTAAAATATTTTATTCAAAAATAAAAT
42687487 AATATTGATTATTCTTTTAAATTTTAGAAACTTCT
66 AATATTGATTATTCTTTTAAATTTTAGAAACTTCT
42687522 TT
1 TT
42687524 AAAGTGCTTA
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 91 0.90
100 10 0.10
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (100 bp):
TTTAAATTAATTTTTATTTATTATTCATGTGAATTTGATTAAAATATTTTATTCAAAAATAAAAT
AATATTGATTATTCTTTTAAATTTTAGAAACTTCT
Found at i:42687566 original size:99 final size:99
Alignment explanation
Indices: 42687353--42687551 Score: 244
Period size: 99 Copynumber: 2.1 Consensus size: 99
42687343 TTATTCATGT
* *
42687353 GAATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTAAATTTTAGAAA
1 GAATTTAATGAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTAAATTTTAGAAA
* ** ** * **
42687418 CTTCTTTTAAATTAATTTTATTTATTATTCATGT
66 CTTCTTTTAAAGTAATTACATACATTATACATCA
* *
42687452 GAATTTGATTAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTAAATTTTAGAAA
1 GAATTTAATGAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTAAATTTTAGAAA
**
42687517 CTTC-TTTAAAGTGCTTACATACA-TA-ACA-CA
66 CTTCTTTTAAAGTAATTACATACATTATACATCA
42687547 GAATT
1 GAATT
42687552 CTAAATAGAC
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
95 5 0.06
96 2 0.02
97 2 0.02
98 12 0.13
99 69 0.77
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (99 bp):
GAATTTAATGAAAATATTTTATTCAAAAATAAAATAATATTGATTATTCTTTTAAATTTTAGAAA
CTTCTTTTAAAGTAATTACATACATTATACATCA
Found at i:42688435 original size:3 final size:3
Alignment explanation
Indices: 42688427--42688464 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42688417 TTTTTTGTCA
42688427 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42688465 ATTAATGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42695700 original size:31 final size:31
Alignment explanation
Indices: 42695665--42695806 Score: 135
Period size: 31 Copynumber: 4.6 Consensus size: 31
42695655 CAACAATATA
* *
42695665 TATATTCATATACGAACCAAATTTGACAATG
1 TATAATCATATACGAATCAAATTTGACAATG
* *
42695696 TAT-ATCTATATACAAATC-AATTCGACAATG
1 TATAATC-ATATACGAATCAAATTTGACAATG
* * *
42695726 TATAACCATATACGAATCAAGTTTGGCAATG
1 TATAATCATATACGAATCAAATTTGACAATG
* * * ** *
42695757 TATAATCATAGACAAATTAAATTCAACAGTG
1 TATAATCATATACGAATCAAATTTGACAATG
*
42695788 TATAACCATATACGAATCA
1 TATAATCATATACGAATCA
42695807 TTTCGACAAC
Statistics
Matches: 86, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
30 26 0.30
31 60 0.70
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (31 bp):
TATAATCATATACGAATCAAATTTGACAATG
Found at i:42695802 original size:62 final size:61
Alignment explanation
Indices: 42695645--42695857 Score: 209
Period size: 61 Copynumber: 3.4 Consensus size: 61
42695635 ATCCAATGCT
* * * * *
42695645 CAAATCAATTCAACAATATATATATTCATATACGAACCAAATTTGACAATGTATATCTATATA
1 CAAATAAATTCAACAATGTATA-A-CCATATACGAATCAAATTTGACAATGTATATCTATAGA
* * * *
42695708 CAAATCAATTCGACAATGTATAACCATATACGAATCAAGTTTGGCAATGTATAATC-ATAGA
1 CAAATAAATTCAACAATGTATAACCATATACGAATCAAATTTGACAATGTAT-ATCTATAGA
* * *
42695769 CAAATTAAATTCAACAGTGTATAACCATATACGAATC--ATTTCGACAACT-TATATCCATATA
1 CAAA-TAAATTCAACAATGTATAACCATATACGAATCAAATTT-GACAA-TGTATATCTATAGA
* *
42695830 CAATTCAATTTCAACAATGTATAACCAT
1 CAAAT-AAATTCAACAATGTATAACCAT
42695858 GTACAAATTA
Statistics
Matches: 128, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
60 7 0.05
61 67 0.52
62 34 0.27
63 20 0.16
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (61 bp):
CAAATAAATTCAACAATGTATAACCATATACGAATCAAATTTGACAATGTATATCTATAGA
Found at i:42695863 original size:31 final size:32
Alignment explanation
Indices: 42695690--42696080 Score: 275
Period size: 31 Copynumber: 12.7 Consensus size: 32
42695680 ACCAAATTTG
* * *
42695690 ACAATGTATATCTATATACAAA-TCAA-TTCG
1 ACAATGTATAACCATATACAAATTCAATTTCA
* *
42695720 ACAATGTATAACCATATACGAA-TCAAGTTT-G
1 ACAATGTATAACCATATACAAATTCAA-TTTCA
* * * *
42695751 GCAATGTATAATCATAGACAAATT-AAATTCA
1 ACAATGTATAACCATATACAAATTCAATTTCA
* * *
42695782 ACAGTGTATAACCATATACGAA-TC-ATTTCG
1 ACAATGTATAACCATATACAAATTCAATTTCA
*
42695812 ACAACT-TATATCCATATAC-AATTCAATTTCA
1 ACAA-TGTATAACCATATACAAATTCAATTTCA
* **
42695843 ACAATGTATAACCATGTACAAATT-AACATCA
1 ACAATGTATAACCATATACAAATTCAATTTCA
* * * *
42695874 GCAATATGTAATCATATACAAA-TCAATTT-A
1 ACAATGTATAACCATATACAAATTCAATTTCA
*
42695904 ACAACT-TATATCCATATAC-AATTCAATTTCA
1 ACAA-TGTATAACCATATACAAATTCAATTTCA
* *
42695935 ATAATGTATAACCATGTACAAATT-AATTTCA
1 ACAATGTATAACCATATACAAATTCAATTTCA
* * *
42695966 GCAATAG-ATAATCATATACAAA-TCAA-TTCG
1 ACAAT-GTATAACCATATACAAATTCAATTTCA
* *
42695996 GCAACT-TATATCCATATAC-AATTCAATTTCA
1 ACAA-TGTATAACCATATACAAATTCAATTTCA
* **
42696027 ACAACGTATAACCATGCACAAATT-AATTTCA
1 ACAATGTATAACCATATACAAATTCAATTTCA
* * * *
42696058 GCAATATACAATCATATACAAAT
1 ACAATGTATAACCATATACAAAT
42696081 CAAGTCGGCC
Statistics
Matches: 280, Mismatches: 57, Indels: 47
0.73 0.15 0.12
Matches are distributed among these distances:
29 6 0.02
30 93 0.33
31 165 0.59
32 16 0.06
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (32 bp):
ACAATGTATAACCATATACAAATTCAATTTCA
Found at i:42696157 original size:92 final size:92
Alignment explanation
Indices: 42695703--42696130 Score: 522
Period size: 92 Copynumber: 4.7 Consensus size: 92
42695693 ATGTATATCT
* * ** *
42695703 ATATACAAATCAATTCGACAA-TGTATAACCATATACGAA-TCAAGTTT-GGCAATGTATAATCA
1 ATATACAAATCAATTCGGCAACT-TATATCCATATAC-AATTCAA-TTTCAACAATGTATAACCA
* * * * *
42695765 TAG-ACAAATTAAATTCAACAGTGTATAACC
63 T-GTACAAATTAATTTCAGCAATATATAATC
* * *
42695795 ATATACGAATCATTTCGACAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
** *
42695860 ACAAATTAACATCAGCAATATGTAATC
66 ACAAATTAATTTCAGCAATATATAATC
*** *
42695887 ATATACAAATCAATTTAACAACTTATATCCATATACAATTCAATTTCAATAATGTATAACCATGT
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
*
42695952 ACAAATTAATTTCAGCAATAGATAATC
66 ACAAATTAATTTCAGCAATATATAATC
* *
42695979 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAACGTATAACCATGC
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
*
42696044 ACAAATTAATTTCAGCAATATACAATC
66 ACAAATTAATTTCAGCAATATATAATC
* * * * **
42696071 ATATACAAATCAAGTCGGCCACTTATATCCATATGCAAATCAATTTTGACAATGTATAAC
1 ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAAC
42696131 TATAAAAAAT
Statistics
Matches: 295, Mismatches: 37, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
91 6 0.02
92 288 0.98
93 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (92 bp):
ATATACAAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATGT
ACAAATTAATTTCAGCAATATATAATC
Found at i:42696159 original size:25 final size:25
Alignment explanation
Indices: 42696131--42696184 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
42696121 AATGTATAAC
*
42696131 TATAAAA-AATTCGAATTCGGCAATA
1 TATAAAACAA-TCAAATTCGGCAATA
*
42696156 TATAAAACAATCAAATTCGGCAATG
1 TATAAAACAATCAAATTCGGCAATA
42696181 TATA
1 TATA
42696185 TCTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (25 bp):
TATAAAACAATCAAATTCGGCAATA
Found at i:42701562 original size:34 final size:34
Alignment explanation
Indices: 42701468--42701563 Score: 111
Period size: 34 Copynumber: 2.8 Consensus size: 34
42701458 ACATTACCAA
* * *
42701468 AAACATATATCCGATCAAAATGCCATATTTCTAG
1 AAACACATATCAGATCAAAATGTCATATTTCTAG
* * *
42701502 AAACATATATCAGATCAAAATATCATATTTTTAG
1 AAACACATATCAGATCAAAATGTCATATTTCTAG
** *
42701536 AAGTACATATCATATCAAAATGTCATAT
1 AAACACATATCAGATCAAAATGTCATAT
42701564 CATATTAGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (34 bp):
AAACACATATCAGATCAAAATGTCATATTTCTAG
Found at i:42709030 original size:18 final size:18
Alignment explanation
Indices: 42709007--42709050 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
42708997 TAGCGACATT
42709007 TTTTAGCGCCGCAAATAC
1 TTTTAGCGCCGCAAATAC
42709025 TTTTAGCGCCGCAAATAC
1 TTTTAGCGCCGCAAATAC
42709043 TTTTAGCG
1 TTTTAGCG
42709051 GCGCTTTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (18 bp):
TTTTAGCGCCGCAAATAC
Found at i:42709221 original size:43 final size:43
Alignment explanation
Indices: 42709173--42709777 Score: 1030
Period size: 43 Copynumber: 14.1 Consensus size: 43
42709163 GCAACGCCGT
* * * *
42709173 TATAGACCAAGGTCTTTAGCGGCGCTTAGCCTAAAAATGTCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
42709216 TATAGACCATGGTCTTTAGCGGCGCTTAGCCGAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* * *
42709259 TATAGATCATTGTCTTTAGCGGCGCTTAGCCACAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
42709302 TATAGACCATGGTCTTTAGCGGCGTTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
42709345 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAATGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* * *
42709388 TAGAGATCATGGTCTTTAGCGGCGCTTAGCCACAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
42709431 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
*
42709474 TATAGATCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* *
42709517 TATAGACCATGGTCTGTAGCGGCGCTTAGACAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
42709560 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* *
42709603 TATAGACCATGGTCTGTAGCGGCGCTTAGACAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
42709646 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
* *
42709689 TATAGACCATGGTCTGTAGCGGCGCTTAGACAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
42709732 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
1 TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
42709775 TAT
1 TAT
42709778 TGCTGATCTG
Statistics
Matches: 527, Mismatches: 35, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 527 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (43 bp):
TATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAAAACGCCAC
Found at i:42709833 original size:21 final size:21
Alignment explanation
Indices: 42709785--42709838 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
42709775 TATTGCTGAT
*
42709785 CTGCTTCCCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCG
*
42709806 CTACTTCCCTCGCTGCAGCCG
1 CTGCTTCCCTCGCTGCAGCCG
*
42709827 CTGCTTCTCTCG
1 CTGCTTCCCTCG
42709839 TTGCCGCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.06, C:0.46, G:0.19, T:0.30
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCG
Found at i:42709919 original size:21 final size:21
Alignment explanation
Indices: 42709890--42709940 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
42709880 TTTCGTTGAA
* *
42709890 CCTCAGCTTCTCTCGCTGCTG
1 CCTCTGCTTCTCTCGCTGCCG
42709911 CCTCTGCTTCTCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCCG
*
42709932 CATCTGCTT
1 CCTCTGCTT
42709941 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCCG
Found at i:42718849 original size:23 final size:23
Alignment explanation
Indices: 42718806--42718850 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42718796 TGGTTTTGTA
*
42718806 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
42718829 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
42718851 AATTAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:42719636 original size:23 final size:23
Alignment explanation
Indices: 42719593--42719637 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42719583 TACTTTTGTA
*
42719593 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
42719616 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
42719638 AATTAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:42720544 original size:41 final size:41
Alignment explanation
Indices: 42720499--42720577 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
42720489 TAGATTTTCT
* * * *
42720499 AATTAGCGGCGTTTTTACACAAACGCTGCTATAGACCGAAG
1 AATTACCGGCGCTGTTACACAAACGCCGCTATAGACCGAAG
*
42720540 AATTACCGGCGCTGTTACACAAATGCCGCTATAGACCG
1 AATTACCGGCGCTGTTACACAAACGCCGCTATAGACCG
42720578 GAACATTAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
AATTACCGGCGCTGTTACACAAACGCCGCTATAGACCGAAG
Found at i:42720718 original size:113 final size:113
Alignment explanation
Indices: 42720590--42720793 Score: 363
Period size: 113 Copynumber: 1.8 Consensus size: 113
42720580 ACATTAGCGG
* *
42720590 GGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATATATGAAAACGGCGTCGTTCTGTGTTACT
1 GGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATATATGAAAACGGCGTCGTTCTGTGTGACT
42720655 CCATTGCGGCGCTTTTTATAAAACGCCGCTGAAGAACGGAGTTTTAGC
66 CCATTGCGGCGCTTTTTATAAAACGCCGCTGAAGAACGGAGTTTTAGC
*
42720703 GGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATATATGAAAACGGCGTTGTTCTGTGTGACT
1 GGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATATATGAAAACGGCGTCGTTCTGTGTGACT
* *
42720768 CTATTGCGGCGCTTTTTGTAAAACGC
66 CCATTGCGGCGCTTTTTATAAAACGC
42720794 TCCTAATGCT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 86 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (113 bp):
GGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATATATGAAAACGGCGTCGTTCTGTGTGACT
CCATTGCGGCGCTTTTTATAAAACGCCGCTGAAGAACGGAGTTTTAGC
Found at i:42723447 original size:23 final size:23
Alignment explanation
Indices: 42723417--42723483 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
42723407 ACATACATTC
42723417 ACGGGTCTTAAATCGAGCCTACG
1 ACGGGTCTTAAATCGAGCCTACG
42723440 ACGGGTCTTAAATCGAGCCTACG
1 ACGGGTCTTAAATCGAGCCTACG
*
42723463 ATGGGTCTTAAATCGAGCCTA
1 ACGGGTCTTAAATCGAGCCTA
42723484 TGAGGCCTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (23 bp):
ACGGGTCTTAAATCGAGCCTACG
Found at i:42726257 original size:16 final size:17
Alignment explanation
Indices: 42726236--42726279 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
42726226 AATGAGTTTT
42726236 ATTTTTATAATTTT-CA
1 ATTTTTATAATTTTACA
*
42726252 ATTTTTATAATTTTATA
1 ATTTTTATAATTTTACA
42726269 ATTTTT-TAATT
1 ATTTTTATAATT
42726280 ATATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTATAATTTTACA
Found at i:42726284 original size:16 final size:17
Alignment explanation
Indices: 42726236--42726285 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
42726226 AATGAGTTTT
42726236 ATTTTTATAATT-T-TCA
1 ATTTTTATAATTATAT-A
*
42726252 ATTTTTATAATTTTATA
1 ATTTTTATAATTATATA
42726269 ATTTTT-TAATTATATA
1 ATTTTTATAATTATATA
42726285 A
1 A
42726286 AAATTAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 22 0.71
17 8 0.26
18 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTATAATTATATA
Found at i:42729946 original size:28 final size:28
Alignment explanation
Indices: 42729926--42729989 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
42729916 TTTTCAGAGT
42729926 TTCCCGATTTAAAGGCTCTTTTATGAGC
1 TTCCCGATTTAAAGGCTCTTTTATGAGC
*
42729954 TTCCCGATTTAAATGCTCTTTTATGAGC
1 TTCCCGATTTAAAGGCTCTTTTATGAGC
*
42729982 TTCTCGAT
1 TTCCCGAT
42729990 ATTGGCTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (28 bp):
TTCCCGATTTAAAGGCTCTTTTATGAGC
Found at i:42730003 original size:24 final size:24
Alignment explanation
Indices: 42729976--42730156 Score: 143
Period size: 24 Copynumber: 7.5 Consensus size: 24
42729966 ATGCTCTTTT
*
42729976 ATGAGCTTCTCGATATTGGCTCGC
1 ATGAGCTTCCCGATATTGGCTCGC
*
42730000 ATGAGCTTCCCGATATTAGCTCGC
1 ATGAGCTTCCCGATATTGGCTCGC
*
42730024 ATGAGCTTCCCGATATTGGCTTGC
1 ATGAGCTTCCCGATATTGGCTCGC
* * * * * *
42730048 TTGAACTTCTCGACATTGACTCGT
1 ATGAGCTTCCCGATATTGGCTCGC
* * *
42730072 ATGAGCTTCCCGTTAATGGCTCTC
1 ATGAGCTTCCCGATATTGGCTCGC
** * *
42730096 CGGAG-TTCCC-ATTACATGGCTCAC
1 ATGAGCTTCCCGA-TA-TTGGCTCGC
*
42730120 ATGAGCTTCCC-ATTATATGGCTCGA
1 ATGAGCTTCCCGA-TAT-TGGCTCGC
*
42730145 AAGAGCTTCCCG
1 ATGAGCTTCCCG
42730157 TTTATATGCT
Statistics
Matches: 122, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
23 7 0.06
24 90 0.74
25 25 0.20
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (24 bp):
ATGAGCTTCCCGATATTGGCTCGC
Found at i:42730139 original size:25 final size:25
Alignment explanation
Indices: 42730072--42730164 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 25
42730062 ATTGACTCGT
* *
42730072 ATGAGCTTCCCGTTA-ATGGCTCTC
1 ATGAGCTTCCCATTATATGGCTCAC
** *
42730096 CGGAG-TTCCCATTACATGGCTCAC
1 ATGAGCTTCCCATTATATGGCTCAC
42730120 ATGAGCTTCCCATTATATGGCTCGA-
1 ATGAGCTTCCCATTATATGGCTC-AC
* *
42730145 AAGAGCTTCCCGTTTATATG
1 ATGAGCTTCCC-ATTATATG
42730165 CTTGTATGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
23 8 0.14
24 14 0.25
25 26 0.46
26 8 0.14
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCATTATATGGCTCAC
Found at i:42730175 original size:25 final size:25
Alignment explanation
Indices: 42730067--42730181 Score: 76
Period size: 25 Copynumber: 4.6 Consensus size: 25
42730057 TCGACATTGA
* *
42730067 CTCGTATGAGCTTCCCGTTA-ATGG
1 CTCGAATGAGCTTCCCATTATATGG
**** *
42730091 CTCTCCGGAG-TTCCCATTACATGG
1 CTCGAATGAGCTTCCCATTATATGG
42730115 CTC-ACATGAGCTTCCCATTATATGG
1 CTCGA-ATGAGCTTCCCATTATATGG
* *
42730140 CTCGAAAGAGCTTCCCGTTTATAT-G
1 CTCGAATGAGCTTCCC-ATTATATGG
* *
42730165 CTTGTATGAGCATTCCC
1 CTCGAATGAGC-TTCCC
42730182 CAATATGAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
23 8 0.11
24 16 0.23
25 35 0.49
26 12 0.17
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (25 bp):
CTCGAATGAGCTTCCCATTATATGG
Found at i:42732245 original size:9 final size:9
Alignment explanation
Indices: 42732231--42732258 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42732221 ACATTCGGCT
42732231 TCAAAGAAA
1 TCAAAGAAA
42732240 TCAAAGAAA
1 TCAAAGAAA
42732249 TCAAAGAAA
1 TCAAAGAAA
42732258 T
1 T
42732259 ATCATGATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (9 bp):
TCAAAGAAA
Found at i:42733202 original size:22 final size:22
Alignment explanation
Indices: 42733177--42733221 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
42733167 ATGTCAATTG
42733177 TTTGTGAATATCCTGATGTATT
1 TTTGTGAATATCCTGATGTATT
42733199 TTTGTGAATATCCTGATGTATT
1 TTTGTGAATATCCTGATGTATT
42733221 T
1 T
42733222 CCCGAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (22 bp):
TTTGTGAATATCCTGATGTATT
Found at i:42737500 original size:25 final size:25
Alignment explanation
Indices: 42737446--42737517 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
42737436 ATTGGCTTGT
* *
42737446 ATGAGCTTCCCGTTAATGGCTCTTC
1 ATGAACTTCCCGTTAATGGCTCTAC
*
42737471 -GGAACTTCCCGTTACATGGCTC-AC
1 ATGAACTTCCCGTTA-ATGGCTCTAC
*
42737495 ATGAACTTCTCGTTATATGGCTC
1 ATGAACTTCCCGTTA-ATGGCTC
42737518 GAAAAAGCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 13 0.33
25 26 0.67
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGAACTTCCCGTTAATGGCTCTAC
Found at i:42740456 original size:15 final size:15
Alignment explanation
Indices: 42740401--42740457 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
42740391 TTTATATTAC
*
42740401 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
42740416 AACATATTTATAATTGT
1 AAAATATTTATTA-T-T
42740433 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
42740450 AAAATATT
1 AAAATATT
42740458 AATGTTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:42743481 original size:61 final size:61
Alignment explanation
Indices: 42743413--42743538 Score: 162
Period size: 61 Copynumber: 2.1 Consensus size: 61
42743403 TATTTTTAAC
* * * * ** *
42743413 TTTTAGAATTAGAACTAAATTGAAAAATTTTGTAAATGTTGGGGGCTAAATTTATTGAATT
1 TTTTAGAACTAAAACTAAAATGAAAAATTTTATAAACATTGAGGGCTAAATTTATTGAATT
* * *
42743474 TTTTAGAACTAAAACTAAAATGACAACTTTTATAAACATTGAGGGCTAAATTTGTTGAATT
1 TTTTAGAACTAAAACTAAAATGAAAAATTTTATAAACATTGAGGGCTAAATTTATTGAATT
42743535 TTTT
1 TTTT
42743539 GGATTTAGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (61 bp):
TTTTAGAACTAAAACTAAAATGAAAAATTTTATAAACATTGAGGGCTAAATTTATTGAATT
Found at i:42743955 original size:11 final size:12
Alignment explanation
Indices: 42743925--42743958 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
42743915 CGGCTAACCC
42743925 ATATTAATTTTT
1 ATATTAATTTTT
42743937 ATATTAATTTTT
1 ATATTAATTTTT
42743949 ATA-TAATTTT
1 ATATTAATTTT
42743959 AATTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:42759110 original size:77 final size:78
Alignment explanation
Indices: 42759022--42759175 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 78
42759012 CGTTAGGGCA
42759022 CAACATTTTATTCTCTTCAAGGTGAGTTAGTCCAAAAAAAAAA-TCGTGTAATAAAATTTAAGAA
1 CAACATTTTATTCTCTTCAAGGTGAGTTAGTCCAAAAAAAAAACTCGTGTAATAAAATTTAAGAA
42759086 AATACTTAATTGC
66 AATACTTAATTGC
42759099 CAACATTTTATTCTCTTCAAGGTGAGTTAGTCCAAAAAAAAAACTCGTGTAATAAAATTTAAGAA
1 CAACATTTTATTCTCTTCAAGGTGAGTTAGTCCAAAAAAAAAACTCGTGTAATAAAATTTAAGAA
42759164 AATACTTAATTG
66 AATACTTAATTG
42759176 TTTAAAATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 43 0.57
78 33 0.43
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (78 bp):
CAACATTTTATTCTCTTCAAGGTGAGTTAGTCCAAAAAAAAAACTCGTGTAATAAAATTTAAGAA
AATACTTAATTGC
Found at i:42759554 original size:15 final size:15
Alignment explanation
Indices: 42759534--42759563 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42759524 ATAGATGTCG
42759534 CAATAACAAATACAA
1 CAATAACAAATACAA
*
42759549 CAATAATAAATACAA
1 CAATAACAAATACAA
42759564 TAACGGCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:42761588 original size:44 final size:44
Alignment explanation
Indices: 42761540--42761624 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
42761530 TAGGAACTAA
*
42761540 AGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAGGATTATT
1 AGCTTCAATCTACTCCACTACAACTTCAGAGAGATAGGATTATT
* * * *
42761584 AGCTTTAATCTGCTCCACTACAATTTCAGGGAGATAGGATT
1 AGCTTCAATCTACTCCACTACAACTTCAGAGAGATAGGATT
42761625 CGCCATCTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
AGCTTCAATCTACTCCACTACAACTTCAGAGAGATAGGATTATT
Found at i:42761970 original size:50 final size:50
Alignment explanation
Indices: 42761916--42762096 Score: 168
Period size: 50 Copynumber: 3.6 Consensus size: 50
42761906 ACTAGGGAGA
*
42761916 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACGCCAGGGAAG
* * * * * ** ** * ** *
42761966 TAAGACTCGCAGTCGCGGCTTCAGTCTTTTAAATTACAATGTTGAGGAAACG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACG-CCAGGGAA-G
* * * *
42762018 --AGATTCACCGTCGTAGCTTCAATCTGTTCCATTATACCGCCAGGGAAG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACGCCAGGGAAG
42762066 TAAGATTCACCGTCGTGGCTTCAATCTGCTC
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTC
42762097 TACTGTAATG
Statistics
Matches: 96, Mismatches: 31, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
48 1 0.01
49 5 0.05
50 84 0.88
51 5 0.05
52 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (50 bp):
TAAGATTCACCGTCGTGGCTTCAATCTGCTCCATTACAACGCCAGGGAAG
Done.