Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 139 of 228
Found at i:41766743 original size:27 final size:28
Alignment explanation
Indices: 41766659--41766756 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
41766649 CATGAGATTG
* * *
41766659 GCACTAAGTGTGC-AGGTTTAAATTGTACA
1 GCACTAAGTGTGCGA-GTTT-GATTATATA
41766688 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41766716 GCACTAAGTGTGTGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41766743 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
41766757 GACTTAATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.37
28 21 0.34
29 17 0.27
30 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41766767 original size:27 final size:27
Alignment explanation
Indices: 41766687--41766769 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
41766677 TAAATTGTAC
* * *
41766687 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGGGA-CTTGAATATAT
* * *
41766715 AGCACTAAGTGTGTGAGTTGATTATAT
1 AGCACTAAGTGTGGGACTTGAATATAT
*
41766742 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTG-GGACTTGAATATAT
41766769 A
1 A
41766770 TTTTTGAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 29 0.60
28 19 0.40
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGGGACTTGAATATAT
Found at i:41778350 original size:20 final size:19
Alignment explanation
Indices: 41778325--41778362 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41778315 AAGAGAAAGG
41778325 GAAAATATGAATAAATATAT
1 GAAAATATGAAT-AATATAT
*
41778345 GAAAATGTGAATAATATA
1 GAAAATATGAATAATATA
41778363 CTTTATGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (19 bp):
GAAAATATGAATAATATAT
Found at i:41786318 original size:30 final size:30
Alignment explanation
Indices: 41786284--41786394 Score: 204
Period size: 30 Copynumber: 3.7 Consensus size: 30
41786274 CCTGACCACA
*
41786284 CCTGACCACACTGCCGTGTGAGGTACACGG
1 CCTGACCACACTGCCGTGTGAGGCACACGG
*
41786314 CCTGACCACACTGCCGTGTGAGGCACACAG
1 CCTGACCACACTGCCGTGTGAGGCACACGG
41786344 CCTGACCACACTGCCGTGTGAGGCACACGG
1 CCTGACCACACTGCCGTGTGAGGCACACGG
41786374 CCTGACCACACTGCCGTGTGA
1 CCTGACCACACTGCCGTGTGA
41786395 CCCCTGATAG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (30 bp):
CCTGACCACACTGCCGTGTGAGGCACACGG
Found at i:41803233 original size:8 final size:8
Alignment explanation
Indices: 41803220--41803250 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
41803210 GAATGAGTGA
41803220 GGGATGAT
1 GGGATGAT
41803228 GGGATGAT
1 GGGATGAT
41803236 GGGATGA-
1 GGGATGAT
41803243 GGGATGAT
1 GGGATGAT
41803251 TGAAAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.26, C:0.00, G:0.52, T:0.23
Consensus pattern (8 bp):
GGGATGAT
Found at i:41803233 original size:23 final size:23
Alignment explanation
Indices: 41803207--41803250 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
41803197 AGAAGAGAAT
41803207 GATGAATGAG-TGAGGGATGATGG
1 GATG-ATGAGATGAGGGATGATGG
*
41803230 GATGATGGGATGAGGGATGAT
1 GATGATGAGATGAGGGATGAT
41803251 TGAAAAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (23 bp):
GATGATGAGATGAGGGATGATGG
Found at i:41803248 original size:15 final size:16
Alignment explanation
Indices: 41803220--41803250 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
41803210 GAATGAGTGA
41803220 GGGATGATGGGATGAT
1 GGGATGATGGGATGAT
41803236 GGGATGA-GGGATGAT
1 GGGATGATGGGATGAT
41803251 TGAAAAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.52, T:0.23
Consensus pattern (16 bp):
GGGATGATGGGATGAT
Found at i:41810804 original size:20 final size:19
Alignment explanation
Indices: 41810779--41810818 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
41810769 TAAGAGCCAA
41810779 AATTATATGATATTTAGAAT
1 AATTATATGAT-TTTAGAAT
* *
41810799 AATTATTTGATTTTATAAT
1 AATTATATGATTTTAGAAT
41810818 A
1 A
41810819 TTAAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
AATTATATGATTTTAGAAT
Found at i:41815680 original size:27 final size:25
Alignment explanation
Indices: 41815631--41815697 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
41815621 TCCGACCCAT
* *
41815631 AGCTCGTGTGAGCAGGCCCATTTTCAC
1 AGCTCGTGTGAGCATG-CCAATTT-AC
* *
41815658 AGCTCGTGTGAGCATTCTAATTTAC
1 AGCTCGTGTGAGCATGCCAATTTAC
*
41815683 AGCTCGTTTGAGCAT
1 AGCTCGTGTGAGCAT
41815698 ACATGTACAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 16 0.46
26 5 0.14
27 14 0.40
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (25 bp):
AGCTCGTGTGAGCATGCCAATTTAC
Found at i:41818082 original size:20 final size:20
Alignment explanation
Indices: 41818049--41818086 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41818039 GTATTCCAAC
* *
41818049 CGAGATTGCTATGTGTAAAT
1 CGAGACTGCCATGTGTAAAT
41818069 CGAGACTGCCATGTGTAA
1 CGAGACTGCCATGTGTAA
41818087 GAGGTTCGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (20 bp):
CGAGACTGCCATGTGTAAAT
Found at i:41828392 original size:34 final size:33
Alignment explanation
Indices: 41828316--41828398 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 33
41828306 CAATTCAATA
41828316 ACAGT-TCAGT-TCAGTTGGGCCTTAGCCCATT
1 ACAGTATCAGTATCAGTTGGGCCTTAGCCCATT
41828347 ACAGTATCAGTATCAGTGTGGGCCTTAGCCCATT
1 ACAGTATCAGTATCAGT-TGGGCCTTAGCCCATT
*
41828381 ACAGTGA-CAGTAACAGTT
1 ACAGT-ATCAGTATCAGTT
41828399 CGGACATGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 6 0.13
34 30 0.64
35 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (33 bp):
ACAGTATCAGTATCAGTTGGGCCTTAGCCCATT
Found at i:41835057 original size:29 final size:29
Alignment explanation
Indices: 41834897--41835064 Score: 160
Period size: 29 Copynumber: 5.8 Consensus size: 29
41834887 AGTTTGAAAC
* * * *
41834897 AAGGCATTCCTTTAATAGAGATGGCCAAA
1 AAGGCATTCTTTTAACAGAGATAGCCATA
* *
41834926 AAGGCA-TCTTTTTAACAGAGATAGCAACA
1 AAGGCATTC-TTTTAACAGAGATAGCCATA
* * *
41834955 AATGAATTCTTTTAATAGAGATAGCCATA
1 AAGGCATTCTTTTAACAGAGATAGCCATA
* * * * *
41834984 AAGGCCTCCTTTGAATAGAGGTAGCC-TCA
1 AAGGCATTCTTTTAACAGAGATAGCCAT-A
41835013 AAGGCATTCTTTTAACAGAGATAGCCATA
1 AAGGCATTCTTTTAACAGAGATAGCCATA
* *
41835042 AAGACATTCTTTTAACAAAGATA
1 AAGGCATTCTTTTAACAGAGATA
41835065 CCCACTGATG
Statistics
Matches: 112, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
28 3 0.03
29 106 0.95
30 3 0.03
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (29 bp):
AAGGCATTCTTTTAACAGAGATAGCCATA
Found at i:41836674 original size:10 final size:10
Alignment explanation
Indices: 41836661--41836698 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41836651 AAGAAGCTAA
41836661 ATTGAGCTCG
1 ATTGAGCTCG
41836671 ATTGAGCT-G
1 ATTGAGCTCG
41836680 ACTTGAGCTCG
1 A-TTGAGCTCG
*
41836691 AGTGAGCT
1 ATTGAGCT
41836699 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:41836685 original size:20 final size:20
Alignment explanation
Indices: 41836662--41836699 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41836652 AGAAGCTAAA
*
41836662 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
41836682 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
41836700 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:41839382 original size:16 final size:15
Alignment explanation
Indices: 41839363--41839416 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 15
41839353 TTTAACTTGA
41839363 TTTTTTTTTGCTCACC
1 TTTTTTTTTGCTCA-C
41839379 TTTTTTTTTTGCTCGA-
1 -TTTTTTTTTGCTC-AC
41839395 TTTTTTTTT--TCAC
1 TTTTTTTTTGCTCAC
41839408 TTTTTTTTT
1 TTTTTTTTT
41839417 TGAATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 11 0.31
15 9 0.26
17 13 0.37
18 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:41839427 original size:29 final size:29
Alignment explanation
Indices: 41839395--41839460 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
41839385 TTTTGCTCGA
* *
41839395 TTTTTTTTT-TCACTTTTTTTTTTGAATT
1 TTTTTTTTTATCAATTTTTTTTTCGAATT
**
41839423 TTTTTTTCAATCAATTTTTTTTTCGAATT
1 TTTTTTTTTATCAATTTTTTTTTCGAATT
41839452 TTTTTTTTT
1 TTTTTTTTT
41839461 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.76
Consensus pattern (29 bp):
TTTTTTTTTATCAATTTTTTTTTCGAATT
Found at i:41839451 original size:13 final size:13
Alignment explanation
Indices: 41839381--41839471 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 13
41839371 TGCTCACCTT
*
41839381 TTTTTTTTGCTCGAT
1 TTTTTTTT--TCGAA
*
41839396 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
*
41839408 TTTTTTTTTTGAA
1 TTTTTTTTTCGAA
*
41839421 TTTTTTTTTCAATCAA
1 TTTTTTTTTC---GAA
41839437 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
*
41839450 TTTTTTTTTTTG-A
1 -TTTTTTTTTCGAA
41839463 TTTTTTTTT
1 TTTTTTTTT
41839472 GTTACTCCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
12 19 0.30
13 15 0.23
14 10 0.16
15 8 0.12
16 12 0.19
ACGTcount: A:0.12, C:0.08, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:41841231 original size:10 final size:10
Alignment explanation
Indices: 41841218--41841255 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41841208 AAGAAGCTAA
41841218 ATTGAGCTCG
1 ATTGAGCTCG
41841228 ATTGAGCT-G
1 ATTGAGCTCG
41841237 ACTTGAGCTCG
1 A-TTGAGCTCG
*
41841248 AGTGAGCT
1 ATTGAGCT
41841256 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:41841242 original size:20 final size:20
Alignment explanation
Indices: 41841219--41841256 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41841209 AGAAGCTAAA
*
41841219 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
41841239 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
41841257 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:41841423 original size:29 final size:29
Alignment explanation
Indices: 41841373--41841484 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
41841363 GCCGTATCAC
* * * *
41841373 CCACAAAGGATTCCTAATAACAAAGTTCG
1 CCACAAAGGCTTCTTTATAACAGAGTTCG
*
41841402 CCACAAAGGCTTCTTTACAACAGAGTTCG
1 CCACAAAGGCTTCTTTATAACAGAGTTCG
* * * * *
41841431 CCACAGAGGCTTTTTTATAATAGAGATCA
1 CCACAAAGGCTTCTTTATAACAGAGTTCG
41841460 CCACAAAGGC-TCTTTTATAACAGAG
1 CCACAAAGGCTTC-TTTATAACAGAG
41841485 ATCACAGCAA
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 1 0.01
29 67 0.99
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (29 bp):
CCACAAAGGCTTCTTTATAACAGAGTTCG
Found at i:41841467 original size:58 final size:59
Alignment explanation
Indices: 41841402--41841536 Score: 150
Period size: 58 Copynumber: 2.3 Consensus size: 59
41841392 ACAAAGTTCG
* * * * *
41841402 CCACAAAGGCTTC-TTTACAACAGAGTTCGCCA-CAGAGGCTTTTTTATAATAGAGATCA
1 CCACAAAGGCTTCTTTTACAACAGAGATC-ACAGCAAAGGATTTCTTATAATAGAGATCA
* * *
41841460 CCACAAAGGC-TCTTTTATAACAGAGATCACAGCAAAGGATTTCTTATAGTAGAGATTA
1 CCACAAAGGCTTCTTTTACAACAGAGATCACAGCAAAGGATTTCTTATAATAGAGATCA
*
41841518 CCACAAACGCTTCATTTTA
1 CCACAAAGGCTTC-TTTTA
41841537 GAGATAGCCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
57 4 0.06
58 53 0.83
59 2 0.03
60 5 0.08
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (59 bp):
CCACAAAGGCTTCTTTTACAACAGAGATCACAGCAAAGGATTTCTTATAATAGAGATCA
Found at i:41841485 original size:29 final size:28
Alignment explanation
Indices: 41841402--41841529 Score: 114
Period size: 29 Copynumber: 4.4 Consensus size: 28
41841392 ACAAAGTTCG
* * *
41841402 CCACAAAGGCTTCTTTACAACAGAGTTCG
1 CCACAAAGGCTT-TTTATAACAGAGATCA
* *
41841431 CCACAGAGGCTTTTTTATAATAGAGATCA
1 CCACAAAGGC-TTTTTATAACAGAGATCA
41841460 CCACAAAGGCTCTTTTATAACAGAGATCA
1 CCACAAAGGCT-TTTTATAACAGAGATCA
* ** *
41841489 -CAGCAAAGGATTTCTTATAGTAGAGATTA
1 CCA-CAAAGGCTTT-TTATAACAGAGATCA
*
41841518 CCACAAACGCTT
1 CCACAAAGGCTT
41841530 CATTTTAGAG
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.06
29 72 0.89
30 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (28 bp):
CCACAAAGGCTTTTTATAACAGAGATCA
Found at i:41842047 original size:17 final size:17
Alignment explanation
Indices: 41842022--41842055 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41842012 TAGTTAGTGG
*
41842022 GATAATGTGGGGGTTAA
1 GATAATGTGGGAGTTAA
*
41842039 GATATTGTGGGAGTTAA
1 GATAATGTGGGAGTTAA
41842056 TTTAATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.32
Consensus pattern (17 bp):
GATAATGTGGGAGTTAA
Found at i:41849798 original size:38 final size:38
Alignment explanation
Indices: 41849718--41849802 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
41849708 GCAATCCTTG
* * * *
41849718 TTATAATTATTGCAATTATAATTTAGGATCGAATATTT
1 TTATAATTACTGCAATTATAATTTAGGATCAAACATTA
* *
41849756 TTATAATTACTGTAATTATAATTTTTGG-TCAAACATTA
1 TTATAATTACTGCAATTATAA-TTTAGGATCAAACATTA
41849794 TTATAATTA
1 TTATAATTA
41849803 TTATATTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
38 35 0.88
39 5 0.12
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (38 bp):
TTATAATTACTGCAATTATAATTTAGGATCAAACATTA
Found at i:41852242 original size:19 final size:18
Alignment explanation
Indices: 41852218--41852253 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41852208 CTCATGCTGA
41852218 TTCTTCTCATCTCATTTTC
1 TTCTTCTC-TCTCATTTTC
*
41852237 TTCTTCTCTCTCCTTTT
1 TTCTTCTCTCTCATTTT
41852254 ATTGGGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (18 bp):
TTCTTCTCTCTCATTTTC
Found at i:41855963 original size:21 final size:21
Alignment explanation
Indices: 41855937--41855978 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41855927 ATTGTTTTAG
41855937 GCTTGAGACA-TATTCCCTTAA
1 GCTTGA-ACAGTATTCCCTTAA
*
41855958 GCTTGAACAGTATTCTCTTAA
1 GCTTGAACAGTATTCCCTTAA
41855979 ATTGGTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (21 bp):
GCTTGAACAGTATTCCCTTAA
Found at i:41857611 original size:60 final size:60
Alignment explanation
Indices: 41857518--41857637 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
41857508 AAAGCTTTTG
* *
41857518 AATTTGTTTTCCTCTAGGTTTGATCTTTGTGAAATTAGGTTTCATTAATTCTCAAAATTT
1 AATTTGTTCTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
* *
41857578 AATTTGTTCTCCTCTAGGTTTGGTCTTAGTGAAATTAGGTTTCATTAATTCTCAGAATTT
1 AATTTGTTCTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
41857638 GAGTTTGTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (60 bp):
AATTTGTTCTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
Found at i:41871991 original size:26 final size:26
Alignment explanation
Indices: 41871958--41872018 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
41871948 CCTATAAGTG
41871958 TTCTAAAACTGATACAT-CTATGATA
1 TTCTAAAACTGATACATGCTATGATA
* *
41871983 TTCTGAAAA-TGATATATGTTATGATA
1 TTCT-AAAACTGATACATGCTATGATA
41872009 TTCTAAAACT
1 TTCTAAAACT
41872019 ACTACAGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (26 bp):
TTCTAAAACTGATACATGCTATGATA
Found at i:41884628 original size:23 final size:24
Alignment explanation
Indices: 41884602--41884646 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41884592 TATAATTATA
*
41884602 TATAT-TATATAATAAGACCCATG
1 TATATGTACATAATAAGACCCATG
*
41884625 TATATGTACATAGTAAGACCCA
1 TATATGTACATAATAAGACCCA
41884647 CGCATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (24 bp):
TATATGTACATAATAAGACCCATG
Found at i:41885982 original size:3 final size:3
Alignment explanation
Indices: 41885919--41885969 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
41885909 AATTAGTCTC
41885919 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41885967 TAT
1 TAT
41885970 GCCCCGATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41890408 original size:13 final size:13
Alignment explanation
Indices: 41890390--41890414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41890380 ATTTACGATC
41890390 TCAAGTTCAATTT
1 TCAAGTTCAATTT
41890403 TCAAGTTCAATT
1 TCAAGTTCAATT
41890415 ACCCATTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (13 bp):
TCAAGTTCAATTT
Found at i:41902173 original size:30 final size:30
Alignment explanation
Indices: 41902081--41902182 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 30
41902071 GGCTATCGAT
*
41902081 TATG-AAAGGGATGGGTGATGACCATC-AAC
1 TATGAAAAGGGAT-GGTGACGACCATCGAAC
*
41902110 AATGAAAAGGGATGGTGACGACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCGAAC
* *
41902140 TATGAAAAGGGATGGCT-TCGACTATC-AATC
1 TATGAAAAGGGATGG-TGACGACCATCGAA-C
41902170 TATGAAAAGGGAT
1 TATGAAAAGGGAT
41902183 AACTTTGGCT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 17 0.27
30 46 0.72
31 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCGAAC
Found at i:41902195 original size:30 final size:31
Alignment explanation
Indices: 41902139--41902205 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
41902129 GACCATCGAA
**
41902139 CTATGAAAAGGGATGGCTTCGACTATC-AAT
1 CTATGAAAAGGGATAACTTCGACTATCAAAT
* *
41902169 CTATGAAAAGGGATAACTTTGGCTATCAAAT
1 CTATGAAAAGGGATAACTTCGACTATCAAAT
41902200 -TATGAA
1 CTATGAA
41902206 TGTACATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (31 bp):
CTATGAAAAGGGATAACTTCGACTATCAAAT
Found at i:41905618 original size:25 final size:25
Alignment explanation
Indices: 41905590--41905637 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
41905580 CAAGCAAGTC
41905590 ATATCAAGAA-GCTCACAAAGAGCCT
1 ATATC-AGAACGCTCACAAAGAGCCT
*
41905615 ATATCAGAACGCTCATAAAGAGC
1 ATATCAGAACGCTCACAAAGAGC
41905638 TGCGATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (25 bp):
ATATCAGAACGCTCACAAAGAGCCT
Found at i:41913249 original size:32 final size:32
Alignment explanation
Indices: 41913189--41913249 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
41913179 CCTTTTTATT
* * *
41913189 AAATTTGGTCATCAACCTTTTTACAAATAGTC
1 AAATTTGATCATCAACCTTTTAAAAAATAGTC
*
41913221 AAATTTGATCATTAACCTTTTAAAAAATA
1 AAATTTGATCATCAACCTTTTAAAAAATA
41913250 ATAAAAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.38
Consensus pattern (32 bp):
AAATTTGATCATCAACCTTTTAAAAAATAGTC
Found at i:41914334 original size:42 final size:42
Alignment explanation
Indices: 41914265--41914344 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
41914255 CTAAATCCTA
* ** *
41914265 AACCTCGAACCCTTAACCATGCGCATTGAATCCCAAACCCCG
1 AACCCCGAACCCTTAACCATGAACATTGAACCCCAAACCCCG
*
41914307 AACCCCGAACCCTTAACCCTGAACATTGAACCCCAAAC
1 AACCCCGAACCCTTAACCATGAACATTGAACCCCAAAC
41914345 TCTTGAATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.34, C:0.41, G:0.10, T:0.15
Consensus pattern (42 bp):
AACCCCGAACCCTTAACCATGAACATTGAACCCCAAACCCCG
Found at i:41914363 original size:29 final size:28
Alignment explanation
Indices: 41914306--41914374 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
41914296 CCCAAACCCC
*
41914306 GAACCCCGAACCCTTAACCCTGAACATT
1 GAACCCCAAACCCTTAACCCTGAACATT
* * *
41914334 GAACCCCAAACTCTTGAATCCTGAATATT
1 GAACCCCAAACCCTT-AACCCTGAACATT
*
41914363 GAACCCCGAACC
1 GAACCCCAAACC
41914375 ACAAACCCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.33, C:0.36, G:0.12, T:0.19
Consensus pattern (28 bp):
GAACCCCAAACCCTTAACCCTGAACATT
Found at i:41918914 original size:42 final size:42
Alignment explanation
Indices: 41918867--41918964 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
41918857 GTCCTCACCC
*** *
41918867 GTGTAACTCACTGAGTAGGGTCACACGGCCGTGT-CGTAGGTT
1 GTGTAACTCACTGAGTAGCCACACACGGCCGTGTAC-TAGGCT
* * *
41918909 GTGTAACTCTCTGAGTTGCCACACATGGCCGTGTACTAGGCT
1 GTGTAACTCACTGAGTAGCCACACACGGCCGTGTACTAGGCT
41918951 GTGTAACTCACTGA
1 GTGTAACTCACTGA
41918965 CTTAAAACAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (42 bp):
GTGTAACTCACTGAGTAGCCACACACGGCCGTGTACTAGGCT
Found at i:41922848 original size:22 final size:22
Alignment explanation
Indices: 41922814--41922868 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41922804 AAAAAAGTAG
*
41922814 GCACCAAAGTGCAAATCAATAA
1 GCACCGAAGTGCAAATCAATAA
* **
41922836 GTACCGAAGTGCAAATCGCTAA
1 GCACCGAAGTGCAAATCAATAA
41922858 GCACCGAAGTG
1 GCACCGAAGTG
41922869 TGAAAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (22 bp):
GCACCGAAGTGCAAATCAATAA
Found at i:41923432 original size:19 final size:20
Alignment explanation
Indices: 41923385--41923433 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
41923375 TACAATATTC
41923385 ATATATTCTTATATTTTTCA
1 ATATATTCTTATATTTTTCA
*
41923405 CTATATTCTT-TATTTTTCA
1 ATATATTCTTATATTTTTCA
*
41923424 ATATTTTCTT
1 ATATATTCTT
41923434 GTAAACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATATTCTTATATTTTTCA
Found at i:41928210 original size:36 final size:37
Alignment explanation
Indices: 41928160--41928229 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
41928150 TTCATATGAA
* *
41928160 TTACTTAATTTTATTATAA-TAT-ATATTATATATAT
1 TTACTTAACTTTATTAAAATTATAATATTATATATAT
*
41928195 TTACTTTAACTTTATTAAAATTTTAATATTATATA
1 TTAC-TTAACTTTATTAAAATTATAATATTATATA
41928230 ACTACTACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 4 0.14
36 13 0.45
37 2 0.07
38 10 0.34
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (37 bp):
TTACTTAACTTTATTAAAATTATAATATTATATATAT
Found at i:41929840 original size:41 final size:41
Alignment explanation
Indices: 41929783--41929865 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
41929773 ATTATGTTGG
41929783 AATGTTCGTGGATTGGGGAGTCCACGGGTAGGCTTCAGCAT
1 AATGTTCGTGGATTGGGGAGTCCACGGGTAGGCTTCAGCAT
*
41929824 AATGTTCGTGGATTGGGGAGTCCACGGGTAGGCTTTAGCAT
1 AATGTTCGTGGATTGGGGAGTCCACGGGTAGGCTTCAGCAT
41929865 A
1 A
41929866 TGCTGAAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.28
Consensus pattern (41 bp):
AATGTTCGTGGATTGGGGAGTCCACGGGTAGGCTTCAGCAT
Found at i:41932537 original size:21 final size:21
Alignment explanation
Indices: 41932513--41932555 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41932503 CTGATTTTAT
41932513 TAGTGCTCAGTTAGGAAATAG
1 TAGTGCTCAGTTAGGAAATAG
41932534 TAGTGCTCAGTTAGGAAATAG
1 TAGTGCTCAGTTAGGAAATAG
41932555 T
1 T
41932556 CCATCGTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (21 bp):
TAGTGCTCAGTTAGGAAATAG
Found at i:41934879 original size:25 final size:26
Alignment explanation
Indices: 41934833--41934885 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
41934823 ATAAAATTGA
41934833 AACAAATCAATATAAATAAAAT-ATT
1 AACAAATCAATATAAATAAAATAATT
* * * *
41934858 AACAAATCGATATTATTTAAATAATT
1 AACAAATCAATATAAATAAAATAATT
41934884 AA
1 AA
41934886 TATTGATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (26 bp):
AACAAATCAATATAAATAAAATAATT
Found at i:41937541 original size:48 final size:48
Alignment explanation
Indices: 41937439--41937635 Score: 225
Period size: 48 Copynumber: 4.1 Consensus size: 48
41937429 AACAGATTTC
** * * * * * *
41937439 TCGGTGGCCTGCACACAGTCCGTATCACCTTTGTGTAATAATAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
* * * *
41937487 TCGGTGGCCTGCACATAGTCTGTGCCACCCTTGTATCTTAACATG-TTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACA-GAATA
* *
41937535 TTGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
* * *
41937583 TCAGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAATAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
41937631 TCGGT
1 TCGGT
41937636 ACGCATAGTA
Statistics
Matches: 125, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
47 1 0.01
48 123 0.98
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
Found at i:41939142 original size:25 final size:25
Alignment explanation
Indices: 41939112--41939161 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
41939102 AATTGTTTGA
*
41939112 ATATGAATATGCAGTGAATTGGATT
1 ATATGAAAATGCAGTGAATTGGATT
*
41939137 ATATGAAAATGTAGTGAATTGGATT
1 ATATGAAAATGCAGTGAATTGGATT
41939162 TCTATGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (25 bp):
ATATGAAAATGCAGTGAATTGGATT
Found at i:41941923 original size:14 final size:14
Alignment explanation
Indices: 41941900--41941933 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41941890 TCCCATTTTC
41941900 AAAA-AAATAAAAT
1 AAAATAAATAAAAT
*
41941913 AAAATAAATAAGAT
1 AAAATAAATAAAAT
41941927 AAAATAA
1 AAAATAA
41941934 CCAAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:41946939 original size:65 final size:64
Alignment explanation
Indices: 41946868--41947015 Score: 210
Period size: 65 Copynumber: 2.3 Consensus size: 64
41946858 CTATGTAAGC
41946868 CTTTATTCTGCCATCACATGCTAGTGCGTCCCACCATGCCTTGACTATTTTTTAATATCACATG
1 CTTTATTCTGCCATCACATGCTAGTGCGTCCCACCATGCCTTGACTATTTTTTAATATCACATG
** * * *
41946932 CTTTTATTCAT-CCATCACATGCTAGTGTTTCCCATCATGCCTTTACTGTTTTTTAATATCACAT
1 C-TTTATTC-TGCCATCACATGCTAGTGCGTCCCACCATGCCTTGACTATTTTTTAATATCACAT
41946996 G
64 G
*
41946997 C-TTATTATGCCATCACATG
1 CTTTATTCTGCCATCACATG
41947016 ATGCCTTTAC
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
62 1 0.01
63 15 0.20
64 1 0.01
65 57 0.76
66 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (64 bp):
CTTTATTCTGCCATCACATGCTAGTGCGTCCCACCATGCCTTGACTATTTTTTAATATCACATG
Found at i:41947785 original size:24 final size:24
Alignment explanation
Indices: 41947736--41947785 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
41947726 CCACTATTAA
* **
41947736 ATGGATTCCTTCTACTCAAGTGTC
1 ATGGATGCCTTCTACTCAAGAATC
*
41947760 ATGGATGCCTTCTACTTAAGAATC
1 ATGGATGCCTTCTACTCAAGAATC
41947784 AT
1 AT
41947786 CTGTCTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (24 bp):
ATGGATGCCTTCTACTCAAGAATC
Found at i:41948426 original size:38 final size:38
Alignment explanation
Indices: 41948349--41948426 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 38
41948339 GAACAATAAT
* *
41948349 AATACCAACAATCACATAAACTGGTTTTCCATTTCAAC
1 AATACCAACAATCACATAAACTGATTTTCCATTTAAAC
* * * **
41948387 AATACCAACATTTACATAAGCTGATTTTTTATTTAAAC
1 AATACCAACAATCACATAAACTGATTTTCCATTTAAAC
41948425 AA
1 AA
41948427 CAAAAAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (38 bp):
AATACCAACAATCACATAAACTGATTTTCCATTTAAAC
Found at i:41953020 original size:3 final size:3
Alignment explanation
Indices: 41953012--41953055 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
41953002 CATTTTAGTG
* *
41953012 TTA TTA TTA TTA TTA TTA TTTA TTA TTA CTA TTAA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT-A TTA TTA TTA
41953056 GTTTCATCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41953036 original size:16 final size:17
Alignment explanation
Indices: 41953015--41953055 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
41953005 TTTAGTGTTA
*
41953015 TTATTATTATTATT-AT
1 TTATTATTACTATTAAT
41953031 TTATTATTACTATTAAT
1 TTATTATTACTATTAAT
41953048 TT-TTATTA
1 TTATTATTA
41953056 GTTTCATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTATTACTATTAAT
Found at i:41953036 original size:19 final size:19
Alignment explanation
Indices: 41953012--41953055 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
41953002 CATTTTAGTG
*
41953012 TTATTATTATTATT-ATTAT
1 TTATTATTACTATTAATT-T
41953031 TTATTATTACTATTAATTT
1 TTATTATTACTATTAATTT
41953050 TTATTA
1 TTATTA
41953056 GTTTCATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATTACTATTAATTT
Found at i:41957747 original size:37 final size:35
Alignment explanation
Indices: 41957687--41957763 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 35
41957677 ATTCAATCAA
*
41957687 AAAAATAAAAATTCAAAATCAAAAAACAAAAAAAGAAG
1 AAAAAGAAAAATTCAAAATC--AAAA-AAAAAAAGAAG
* *
41957725 AAAAAGAAAAA-TCAAAGTCAAAAGAAAAAAGAAG
1 AAAAAGAAAAATTCAAAATCAAAAAAAAAAAGAAG
41957759 AAAAA
1 AAAAA
41957764 TCAATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 15 0.42
35 4 0.11
37 7 0.19
38 10 0.28
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.08
Consensus pattern (35 bp):
AAAAAGAAAAATTCAAAATCAAAAAAAAAAAGAAG
Found at i:41957784 original size:38 final size:37
Alignment explanation
Indices: 41957687--41957813 Score: 105
Period size: 38 Copynumber: 3.3 Consensus size: 37
41957677 ATTCAATCAA
*
41957687 AAAAATAAAAATTCAAAATCAAAAAACAAAAAAAGAAG
1 AAAAAGAAAAA-TCAAAATCAAAAAACAAAAAAAGAAG
* *
41957725 AAAAAGAAAAATCAAAGTCAAAAGAA-AAAAGAAGAA-
1 AAAAAGAAAAATCAAAATCAAAA-AACAAAAAAAGAAG
** * *
41957761 AAATCAATCAAAATCAAAATCAAAATCAAAATAAAAAAAGGAG
1 AAA--AAGAAAAATCAAAATC--AA--AAAACAAAAAAAGAAG
41957804 AAAAAGAAAA
1 AAAAAGAAAA
41957814 GGAGAGGCTA
Statistics
Matches: 70, Mismatches: 10, Indels: 15
0.74 0.11 0.16
Matches are distributed among these distances:
36 3 0.04
37 20 0.29
38 25 0.36
40 2 0.03
41 7 0.10
42 10 0.14
43 3 0.04
ACGTcount: A:0.74, C:0.08, G:0.09, T:0.09
Consensus pattern (37 bp):
AAAAAGAAAAATCAAAATCAAAAAACAAAAAAAGAAG
Found at i:41957797 original size:6 final size:6
Alignment explanation
Indices: 41957766--41957796 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
41957756 AAGAAAAATC
41957766 AATCAA AATCAA AATCAA AATCAA AAT-AA AA
1 AATCAA AATCAA AATCAA AATCAA AATCAA AA
41957797 AAAGGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (6 bp):
AATCAA
Found at i:41959029 original size:19 final size:19
Alignment explanation
Indices: 41959005--41959048 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
41958995 TATTTTAGTG
* *
41959005 TTATTATTATTATTATTTT
1 TTATTATTACTATTAATTT
41959024 TTATTATTACTATTAATTT
1 TTATTATTACTATTAATTT
41959043 TTATTA
1 TTATTA
41959049 GTTTCATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTACTATTAATTT
Found at i:41961718 original size:27 final size:27
Alignment explanation
Indices: 41961688--41961837 Score: 133
Period size: 27 Copynumber: 5.5 Consensus size: 27
41961678 AAATTGTACA
*
41961688 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
* ** * *
41961715 GCACTCAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
41961742 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
* * *
41961769 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
41961797 GCACTAAGTGTGCGATTTGA-T-TGTAT
1 GCACTAAGTGTGCGATTTGACTATGT-T
*
41961823 AGCACTGAGTGTGCG
1 -GCACTAAGTGTGCG
41961838 GGCTCAATAT
Statistics
Matches: 98, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 73 0.74
28 21 0.21
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:41961755 original size:54 final size:55
Alignment explanation
Indices: 41961687--41961837 Score: 150
Period size: 54 Copynumber: 2.8 Consensus size: 55
41961677 TAAATTGTAC
* *
41961687 AGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAAT-GAA-TATG-
1 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCG-AATCGAACTATGT
* * ** * *
41961740 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAATCGAACTATGT
*
41961796 AGCACTAAGTGTGCGATTTGA-T-TGTATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGATTTGACTATGT-T-GCACTAAGTGTGCG
41961838 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
53 5 0.06
54 37 0.47
55 36 0.46
56 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAATCGAACTATGT
Found at i:41969978 original size:16 final size:15
Alignment explanation
Indices: 41969957--41969998 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
41969947 GCATAACATT
*
41969957 TTTATTTTATCTTTTA
1 TTTATTTT-TCATTTA
41969973 TTTATTTGTTCATTTA
1 TTTATTT-TTCATTTA
41969989 TTTATTTTTC
1 TTTATTTTTC
41969999 TATCATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.83
17 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTATTTTTCATTTA
Found at i:41971285 original size:27 final size:27
Alignment explanation
Indices: 41971231--41971289 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
41971221 ATATGCTGGA
* *
41971231 GGCTTCTTTAGAGGTTCATGGATTGGT
1 GGCTTCTTTAGAGGTTCATAGATCGGT
* *
41971258 GGCTTCTTTGGAGGTTCATATATCGGT
1 GGCTTCTTTAGAGGTTCATAGATCGGT
41971285 GGCTT
1 GGCTT
41971290 GTGTTCTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.32, T:0.41
Consensus pattern (27 bp):
GGCTTCTTTAGAGGTTCATAGATCGGT
Found at i:41971412 original size:48 final size:48
Alignment explanation
Indices: 41971360--41971474 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
41971350 ATGAATCGGT
* * ** *
41971360 GGCTTCTTTGGAAATTCATGGAGTGGTGGTTTATGTTTATACATTGGA
1 GGCTTCTTTGGAAGTTCATGGAGTGATGGCGTAGGTTTATACATTGGA
* * *
41971408 GGCTTCTTTAGAGGTTCATGGATTGATGGCGTAGGTTTATACATTGGA
1 GGCTTCTTTGGAAGTTCATGGAGTGATGGCGTAGGTTTATACATTGGA
*
41971456 GGCTTATTTGGAAGTTCAT
1 GGCTTCTTTGGAAGTTCAT
41971475 CTGATGGTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.21, C:0.10, G:0.30, T:0.40
Consensus pattern (48 bp):
GGCTTCTTTGGAAGTTCATGGAGTGATGGCGTAGGTTTATACATTGGA
Found at i:41982608 original size:51 final size:51
Alignment explanation
Indices: 41982529--41982628 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
41982519 TTAATGAATC
41982529 CTATGTACAAAAGTTTTTAAAAAAAATATTTATACATGAACTCAAAATAAA
1 CTATGTACAAAAGTTTTTAAAAAAAATATTTATACATGAACTCAAAATAAA
*
41982580 CTATGTACAAAAGTTCTTT-AAAATAATATTTATACATGAACTCAAAATA
1 CTATGTACAAAAGTT-TTTAAAAAAAATATTTATACATGAACTCAAAATA
41982629 GACTTGAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 44 0.94
52 3 0.06
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (51 bp):
CTATGTACAAAAGTTTTTAAAAAAAATATTTATACATGAACTCAAAATAAA
Found at i:41983994 original size:17 final size:19
Alignment explanation
Indices: 41983963--41983997 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
41983953 ACTAATGAAT
41983963 AAAAGAGAAGAAAATCTAG
1 AAAAGAGAAGAAAATCTAG
41983982 AAAAGA-AAG-AAATCTA
1 AAAAGAGAAGAAAATCTA
41983998 AAATCACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAAGAGAAGAAAATCTAG
Found at i:41991267 original size:18 final size:17
Alignment explanation
Indices: 41991236--41991277 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
41991226 TTGTTTGTAT
41991236 ATTTTTTTCA-TTTTATA
1 ATTTTTTTCATTTTTA-A
*
41991253 ATTTTTATTCCTTTTTAA
1 ATTTTT-TTCATTTTTAA
41991271 ATTTTTT
1 ATTTTTT
41991278 AATTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 5 0.23
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTCATTTTTAA
Found at i:42006020 original size:37 final size:37
Alignment explanation
Indices: 42005979--42006073 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 37
42005969 TACTCCCTAT
* * *
42005979 TTTGGCTTGTTATCGGGTGGATTAGCTCTTATGAGCA
1 TTTGGCGTGTTATCGGTTGGATTAACTCTTATGAGCA
* * * *
42006016 TTTGGCGTGTTTTCCGTTGGATTAACTGTTATGAGCG
1 TTTGGCGTGTTATCGGTTGGATTAACTCTTATGAGCA
42006053 TTTGGCGTGTTATCGGTTGGA
1 TTTGGCGTGTTATCGGTTGGA
42006074 CTACTGTGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.14, C:0.13, G:0.32, T:0.42
Consensus pattern (37 bp):
TTTGGCGTGTTATCGGTTGGATTAACTCTTATGAGCA
Found at i:42014967 original size:61 final size:61
Alignment explanation
Indices: 42014895--42015010 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
42014885 TTTAATATTT
* *
42014895 AATTTAATTTAATAGTTATGTTGATTGTATTTTACTAATTTAATATTAATGTGAGCTGTTA
1 AATTTAATTTAATAGTTATCTTGATAGTATTTTACTAATTTAATATTAATGTGAGCTGTTA
* * * *
42014956 AATTTGATTTAATATTTATCTTTATAGTATTTTATTAATTTAATATTAATGTGAG
1 AATTTAATTTAATAGTTATCTTGATAGTATTTTACTAATTTAATATTAATGTGAG
42015011 TAATTTCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (61 bp):
AATTTAATTTAATAGTTATCTTGATAGTATTTTACTAATTTAATATTAATGTGAGCTGTTA
Found at i:42018031 original size:13 final size:13
Alignment explanation
Indices: 42018013--42018038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42018003 TAAATTAATA
42018013 CGTGTGAAAATTT
1 CGTGTGAAAATTT
42018026 CGTGTGAAAATTT
1 CGTGTGAAAATTT
42018039 TATTATTTGT
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:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
CGTGTGAAAATTT
Found at i:42019261 original size:43 final size:43
Alignment explanation
Indices: 42019144--42019270 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 43
42019134 TAGGATTCAT
*
42019144 TTATGTGTTATCGTGTAAAACCACGTCTGGGACGTTGGCATCAA
1 TTATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCAA
* * *
42019188 CT-TGTGTTTACGTGTAAGACC-CTGTTTGGGACAG-TGGCATC-G
1 TTATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAA
* *
42019230 TTATGTGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 TTATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
42019271 TGTACGATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
42 3 0.04
43 59 0.87
44 6 0.09
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TTATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCATCAA
Found at i:42020279 original size:23 final size:23
Alignment explanation
Indices: 42020248--42020447 Score: 240
Period size: 23 Copynumber: 8.7 Consensus size: 23
42020238 ATTGGGTATA
* * *
42020248 TATATATGCTGTCAAATTTTGTG
1 TATAAATGCTGTCCAATTTGGTG
*
42020271 TATAAATGCTGTCCAATTTAGTG
1 TATAAATGCTGTCCAATTTGGTG
*
42020294 TATATATGCTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
42020317 TATAAATGTTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
**
42020340 TATAAATATTGTCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* *
42020363 TATATATGCTGTCCAATTTGGTA
1 TATAAATGCTGTCCAATTTGGTG
* *
42020386 TATATATGCTGTCCAATTGGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * * *
42020409 TATAAATGATGTTCGATTTGATG
1 TATAAATGCTGTCCAATTTGGTG
42020432 TATAAGA-GCTGTCCAA
1 TATAA-ATGCTGTCCAA
42020448 ACAGGGTAGA
Statistics
Matches: 153, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
23 152 0.99
24 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (23 bp):
TATAAATGCTGTCCAATTTGGTG
Found at i:42020428 original size:69 final size:69
Alignment explanation
Indices: 42020246--42020435 Score: 265
Period size: 69 Copynumber: 2.8 Consensus size: 69
42020236 TGATTGGGTA
* * * *
42020246 TATATATATGCTGTCAAATTTTGTGTATAAATGCTGTCCAATTTAGTGTATATATGCTGTCCAAT
1 TATATATATGCTGTCCAATTTGGTGTATAAATGATGTCCAATTTGGTGTATATATGCTGTCCAAT
42020311 TTGG
66 TTGG
* * *
42020315 TGTATAAATGTTGTCCAATTTGGTGTATAAAT-ATTGTCCAATTTGGTGTATATATGCTGTCCAA
1 TATATATATGCTGTCCAATTTGGTGTATAAATGA-TGTCCAATTTGGTGTATATATGCTGTCCAA
42020379 TTTGG
65 TTTGG
* * * *
42020384 TATATATATGCTGTCCAATTGGGTGTATAAATGATGTTCGATTTGATGTATA
1 TATATATATGCTGTCCAATTTGGTGTATAAATGATGTCCAATTTGGTGTATA
42020436 AGAGCTGTCC
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
69 104 0.99
70 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.43
Consensus pattern (69 bp):
TATATATATGCTGTCCAATTTGGTGTATAAATGATGTCCAATTTGGTGTATATATGCTGTCCAAT
TTGG
Found at i:42022670 original size:20 final size:20
Alignment explanation
Indices: 42022643--42022701 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
42022633 CTATCTTCCA
42022643 CTTT-TTTATTCTATATTTT
1 CTTTATTTATTCTATATTTT
*
42022662 CTTTATTTAGT-TATTATTTT
1 CTTTATTTATTCTA-TATTTT
*** *
42022682 GAATATTTATTCTTTATTTT
1 CTTTATTTATTCTATATTTT
42022702 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 6 0.19
20 24 0.77
21 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.69
Consensus pattern (20 bp):
CTTTATTTATTCTATATTTT
Found at i:42025255 original size:24 final size:24
Alignment explanation
Indices: 42025223--42025279 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
42025213 TTCAACATGC
*
42025223 GGAGGTTTACCCCCTGAATGTCGT
1 GGAGGTTTACCACCTGAATGTCGT
* *
42025247 GGAGGTTTACCACCTGATTGTTGT
1 GGAGGTTTACCACCTGAATGTCGT
42025271 GGAGGTTTA
1 GGAGGTTTA
42025280 TGTGTGCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.33
Consensus pattern (24 bp):
GGAGGTTTACCACCTGAATGTCGT
Found at i:42025325 original size:171 final size:170
Alignment explanation
Indices: 42024959--42025552 Score: 872
Period size: 171 Copynumber: 3.4 Consensus size: 170
42024949 CTCACTTAAG
*
42024959 AGGTGTCTATGAGGAGGTTTAGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTGTC
1 AGGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTGTC
* ** * * *** *
42025024 ACCGGGGAATGGTT--TCAT-GGATGGCTTACCGTCAGGGAATCCTTCAACATGTGGAGGTTTAC
66 ACCAGGGAATCCTTCAACATGGGA-GGTTTACC--CCCTGAAT--GT---C--GTGGAGGTTTAC
* * * *
42025086 CCCCTGAGTGTCGTGGAGGTTTATGTGTGTCCTCAACTTCCACATTCAAT
121 CACCTGAGTGTTGTGGAGGTTTATGTGTGCCCTCAACTTCCACACTCAAT
42025136 AGGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTGTC
1 AGGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTGTC
*
42025201 ACCAGGGAATCCTTCAACATGCGGAGGTTTACCCCCTGAATGTCGTGGAGGTTTACCACCTGATT
66 ACCAGGGAATCCTTCAACATG-GGAGGTTTACCCCCTGAATGTCGTGGAGGTTTACCACCTGAGT
42025266 GTTGTGGAGGTTTATGTGTGCCCTCAACTTCCACACTCAAT
130 GTTGTGGAGGTTTATGTGTGCCCTCAACTTCCACACTCAAT
*
42025307 AGGTGTCTGTGAGGAGGTTTGGGTTCATGAGGTGC-CCCTTTTCCCTTACCCTTGGATGGTTTGT
1 AGGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCC-TTTCCCTTACCCTTGGATGGTTTGT
42025371 CACCAGGGAATCCTTCAACATGTGGAGGTTTACCCCCTGAATGTCGTGGAGGTTTACCACCTGAG
65 CACCAGGGAATCCTTCAACATG-GGAGGTTTACCCCCTGAATGTCGTGGAGGTTTACCACCTGAG
*
42025436 TGCTGTGGAGGTTTATGTGTGCCCTCAACTTCCACACTCAAT
129 TGTTGTGGAGGTTTATGTGTGCCCTCAACTTCCACACTCAAT
* *
42025478 AAGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTTTC
1 AGGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTGTC
42025543 ACCAGGGAAT
66 ACCAGGGAAT
42025553 GGCTTCATGG
Statistics
Matches: 389, Mismatches: 22, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
170 3 0.01
171 288 0.74
172 3 0.01
173 1 0.00
176 1 0.00
177 75 0.19
178 5 0.01
179 3 0.01
180 7 0.02
181 3 0.01
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.32
Consensus pattern (170 bp):
AGGTGTCTATGAGGAGGTTTGGGTTCATGAGGTGCTCCCTTTCCCTTACCCTTGGATGGTTTGTC
ACCAGGGAATCCTTCAACATGGGAGGTTTACCCCCTGAATGTCGTGGAGGTTTACCACCTGAGTG
TTGTGGAGGTTTATGTGTGCCCTCAACTTCCACACTCAAT
Found at i:42025419 original size:24 final size:24
Alignment explanation
Indices: 42025391--42025450 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
42025381 TCCTTCAACA
*
42025391 TGTGGAGGTTTACCCCCTGAATG-
1 TGTGGAGGTTTACCACCTGAATGC
*
42025414 TCGTGGAGGTTTACCACCTGAGTGC
1 T-GTGGAGGTTTACCACCTGAATGC
42025439 TGTGGAGGTTTA
1 TGTGGAGGTTTA
42025451 TGTGTGCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.17, C:0.18, G:0.33, T:0.32
Consensus pattern (24 bp):
TGTGGAGGTTTACCACCTGAATGC
Found at i:42025621 original size:24 final size:24
Alignment explanation
Indices: 42025593--42025651 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
42025583 CCCTCAACAT
* *
42025593 GTGGAGGTTTACCCCCCGAGTGTC
1 GTGGAGGTTTACCACCCGAATGTC
* *
42025617 TTGGAGGTTTACCACCTGAATGTC
1 GTGGAGGTTTACCACCCGAATGTC
42025641 GTGGAGGTTTA
1 GTGGAGGTTTA
42025652 TGTGTGCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (24 bp):
GTGGAGGTTTACCACCCGAATGTC
Found at i:42027581 original size:21 final size:21
Alignment explanation
Indices: 42027566--42027608 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42027556 TTATTTTAAA
42027566 AAAATATTATAATATTAATAT
1 AAAATATTATAATATTAATAT
*
42027587 AAAATATTATAATTTTCAATAT
1 AAAATATTATAATATT-AATAT
42027609 GATTAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATATTATAATATTAATAT
Found at i:42027657 original size:9 final size:9
Alignment explanation
Indices: 42027631--42027672 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
42027621 ATATTTAATC
42027631 ATATAA-TA
1 ATATAATTA
*
42027639 A-ATTATTA
1 ATATAATTA
42027647 ATATAATTA
1 ATATAATTA
*
42027656 ATATAAATA
1 ATATAATTA
42027665 ATATAATT
1 ATATAATT
42027673 TATTATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
7 3 0.11
8 4 0.14
9 21 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATAATTA
Found at i:42027659 original size:25 final size:25
Alignment explanation
Indices: 42027631--42027698 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
42027621 ATATTTAATC
42027631 ATATAATAAATTATTAATATAATTA
1 ATATAATAAATTATTAATATAATTA
*
42027656 ATATAA-ATAA-TA-TAAT-TTATTA
1 ATATAATA-AATTATTAATATAATTA
* *
42027678 TTTTAATAAATTATTTAATAT
1 ATATAATAAATTA-TTAATAT
42027699 TTTAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
22 11 0.32
23 7 0.21
24 3 0.09
25 12 0.35
26 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATAATAAATTATTAATATAATTA
Found at i:42027748 original size:16 final size:17
Alignment explanation
Indices: 42027712--42027748 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
42027702 AATTTTATTT
*
42027712 TAATAATAAATTTTGAA
1 TAATAATAAATTTTAAA
42027729 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
42027744 TAATA
1 TAATA
42027749 TTCTTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:42034498 original size:43 final size:43
Alignment explanation
Indices: 42034435--42034738 Score: 294
Period size: 43 Copynumber: 7.1 Consensus size: 43
42034425 AATAAATGCC
*
42034435 GCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGTCA
1 GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACG-CA
* * *
42034479 G-TATAGATCAAGACCTTTAGCGGCACTTTTTCCAAAAACGCC
1 GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCA
* * * *
42034521 GCTATAGATTAGGACCTTTAGCGGCGCTTTT-CCACAAACGCC
1 GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCA
* * * * * *
42034563 GCTATAGTTTAAGATCTTTAGCGGCACTTTTTCTACAAACGCT
1 GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCA
* * *
42034606 GCTATAAATCAAGACCTTTAGCGGCATTTTTCCAACAAACGCCA
1 GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACG-CA
* * ***
42034650 -CTATAGATCAAGACCTTTAGCGCCGCTTTTTGATACAAACGCCA
1 GCTATAGATCAAGACCTTTAGCGGCAC-TTTTCCCACAAACG-CA
* * * * *
42034694 -CTATAGAAC-AGACCTTTAGCGGCGCTTTTCACAAAAACGCC
1 GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCA
42034735 GCTA
1 GCTA
42034739 AAAACATATC
Statistics
Matches: 220, Mismatches: 35, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.00
42 53 0.24
43 142 0.65
44 24 0.11
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
GCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCA
Found at i:42034665 original size:128 final size:128
Alignment explanation
Indices: 42034432--42034732 Score: 374
Period size: 128 Copynumber: 2.3 Consensus size: 128
42034422 TGAAATAAAT
* *
42034432 GCCGCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGTCAGTATAGATCAAGACCTTT
1 GCCGCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGTCAGTATAAATCAAGACCTTT
* * * *
42034497 AGCGGCACTTTTTCCAAAAACGCCGCTATAGATTAGGACCTTTAGCGGCGCTTTTCCACAAAC
66 AGCGGCACTTTTTCCAAAAACGCCACTATAGATCAAGACCTTTAGCGCCGCTTTTCCACAAAC
* * * * * *
42034560 GCCGCTATAGTTTAAGATCTTTAGCGGCACTTTTTCTACAAACG-CTGCTATAAATCAAGACCTT
1 GCCGCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGTCAG-TATAAATCAAGACCTT
**
42034624 TAGCGGCA-TTTTTCCAACAAACGCCACTATAGATCAAGACCTTTAGCGCCGCTTTTTGATACAA
65 TAGCGGCACTTTTTCCAA-AAACGCCACTATAGATCAAGACCTTTAGCGCCGC-TTTT-CCACAA
42034688 AC
127 AC
* * * * *
42034690 GCCACTATAGAAC-AGACCTTTAGCGGCGCTTTTCACAAAAACG
1 GCCGCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACG
42034733 CCGCTAAAAA
Statistics
Matches: 145, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
127 11 0.08
128 91 0.63
129 28 0.19
130 15 0.10
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (128 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGTCAGTATAAATCAAGACCTTT
AGCGGCACTTTTTCCAAAAACGCCACTATAGATCAAGACCTTTAGCGCCGCTTTTCCACAAAC
Found at i:42034707 original size:86 final size:86
Alignment explanation
Indices: 42034432--42034734 Score: 344
Period size: 86 Copynumber: 3.5 Consensus size: 86
42034422 TGAAATAAAT
* * * * *
42034432 GCCGCTATAGATCATGACCTTTAGCGGCACTTTTCCCACAAACGTCAGTATAGATCAAGACCTTT
1 GCCGCTATAGAACAGGACCTTTAGCGGCACTTTTCCAACAAACGCCACTATAGATCAAGACCTTT
** *
42034497 AGCGGCACTTTTTCCAAAAAC
66 AGCGGCACTTTTTATACAAAC
** * * * * *
42034518 GCCGCTATAGATTAGGACCTTTAGCGGCGCTTTTCC-ACAAACGCCGCTATAGTTTAAGATCTTT
1 GCCGCTATAGAACAGGACCTTTAGCGGCACTTTTCCAACAAACGCCACTATAGATCAAGACCTTT
*
42034582 AGCGGCACTTTTTCTACAAAC
66 AGCGGCACTTTTTATACAAAC
* * *
42034603 GCTGCTATA-AATCAAGACCTTTAGCGGCATTTTTCCAACAAACGCCACTATAGATCAAGACCTT
1 GCCGCTATAGAA-CAGGACCTTTAGCGGCACTTTTCCAACAAACGCCACTATAGATCAAGACCTT
* *
42034667 TAGCGCCGCTTTTTGATACAAAC
65 TAGCGGCACTTTTT-ATACAAAC
* *
42034690 GCCACTATAGAACA-GACCTTTAGCGGCGCTTTTCACAA-AAACGCC
1 GCCGCTATAGAACAGGACCTTTAGCGGCACTTTTC-CAACAAACGCC
42034735 GCTAAAAACA
Statistics
Matches: 184, Mismatches: 28, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
84 1 0.01
85 69 0.38
86 93 0.51
87 19 0.10
88 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (86 bp):
GCCGCTATAGAACAGGACCTTTAGCGGCACTTTTCCAACAAACGCCACTATAGATCAAGACCTTT
AGCGGCACTTTTTATACAAAC
Found at i:42038378 original size:21 final size:20
Alignment explanation
Indices: 42038354--42038407 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
42038344 ATCGCTGAAT
42038354 CTCTAAACCCTAA-ATCCATAA
1 CTCTAAACCCTAACAT-C-TAA
*
42038375 CTCTTAACCCCTAACATCTAA
1 CTC-TAAACCCTAACATCTAA
42038396 CTCCTAAACCCT
1 CT-CTAAACCCT
42038408 TAGCCCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 15 0.54
22 11 0.39
23 2 0.07
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.26
Consensus pattern (20 bp):
CTCTAAACCCTAACATCTAA
Found at i:42038449 original size:20 final size:21
Alignment explanation
Indices: 42038409--42038449 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42038399 CTAAACCCTT
*
42038409 AGCCCATAAACCTTAAATCCC
1 AGCCCATAAACCATAAATCCC
*
42038430 AGCCCTTAAACCAT-AATCCC
1 AGCCCATAAACCATAAATCCC
42038450 TAAATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.20
Consensus pattern (21 bp):
AGCCCATAAACCATAAATCCC
Found at i:42038983 original size:16 final size:16
Alignment explanation
Indices: 42038946--42038987 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42038936 TTAATCATAT
*
42038946 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
42038962 TT-AAATATATTATAA
1 TTAAAATATATTATAA
42038977 TTAAAATATAT
1 TTAAAATATAT
42038988 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:42038994 original size:14 final size:15
Alignment explanation
Indices: 42038955--42038996 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42038945 TTTAAACATA
*
42038955 ATTATTATTAAATAT
1 ATTATAATTAAATAT
42038970 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
42038984 A-TATAATTTAATA
1 ATTATAATTAAATA
42038997 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:42039063 original size:15 final size:14
Alignment explanation
Indices: 42039040--42039106 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 14
42039030 TACTCAAATC
*
42039040 ATAATATATAATACT
1 ATAAAATATAATA-T
42039055 ATAAAATATAAT-T
1 ATAAAATATAATAT
42039068 -TAAAATA-AATATT
1 ATAAAATATAATA-T
* *
42039081 ATTAAATATAATTT
1 ATAAAATATAATAT
42039095 AATAAAAATATA
1 -AT-AAAATATA
42039107 TAATTTAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
11 3 0.07
12 7 0.17
13 2 0.05
14 7 0.17
15 16 0.38
16 7 0.17
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAAATATAATAT
Found at i:42039078 original size:26 final size:25
Alignment explanation
Indices: 42039049--42039109 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
42039039 CATAATATAT
42039049 AATACTATAAAATATAATTTAA-AATA
1 AATA-TATAAAATATAATTTAATAA-A
*
42039075 AATATTATTAAATATAATTTAATAAA
1 AATA-TATAAAATATAATTTAATAAA
42039101 AATATATAA
1 AATATATAA
42039110 TTTAATCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 25 0.81
27 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATATAAAATATAATTTAATAAA
Found at i:42039269 original size:27 final size:28
Alignment explanation
Indices: 42039239--42039297 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
42039229 TAAATATAGT
*
42039239 AATG-AAGAATTTATAGTATACGATTAA
1 AATGCAAGAATTTATAGTATACAATTAA
*
42039266 AATGCTAATAATTTATAGTATACAATTAA
1 AATGC-AAGAATTTATAGTATACAATTAA
42039295 AAT
1 AAT
42039298 ATTATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
29 24 0.86
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (28 bp):
AATGCAAGAATTTATAGTATACAATTAA
Found at i:42039351 original size:16 final size:17
Alignment explanation
Indices: 42039325--42039362 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
42039315 AGTAAATGAT
42039325 ATATAAGATAAATTAAC
1 ATATAAGATAAATTAAC
42039342 ATATAA-ATAAATTAAC
1 ATATAAGATAAATTAAC
*
42039358 TTATA
1 ATATA
42039363 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (17 bp):
ATATAAGATAAATTAAC
Found at i:42042481 original size:5 final size:5
Alignment explanation
Indices: 42042471--42042496 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42042461 TCGATTTTAC
42042471 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
42042497 ACAGGGAAAA
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:42044021 original size:114 final size:114
Alignment explanation
Indices: 42043805--42044150 Score: 531
Period size: 114 Copynumber: 3.0 Consensus size: 114
42043795 GCGGCGCTTT
* * * *
42043805 AAGCTCTGAGAATTAACGGCGCTATTTTAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAACA--
1 AAGCTCTGAGCATTAGCGGCGCT-TTTTAAAAACTCCGCTAAAGCCCTGAAAGGTCAAAAAAATG
42043868 ATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTA
65 ATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTA
* *
42043918 AAGCTTTGAGCATTAGCGGCGCTTTTTCAAAAACTCCACTAAAGCCCTGAAAGGT-AAAAAAATG
1 AAGCTCTGAGCATTAGCGGCGCTTTTT-AAAAACTCCGCTAAAGCCCTGAAAGGTCAAAAAAATG
42043982 ATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTA
65 ATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTA
42044032 AAGCTCTGAGCATTAGCGGCGCTTTTTTAAATAAGCT--GCTAAAGCCCTGAAAGGTCAAAAAAA
1 AAGCTCTGAGCATTAGCGGCGC-TTTTTAAA-AA-CTCCGCTAAAGCCCTGAAAGGTCAAAAAAA
* * *
42044095 TGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCTAAAAAATGTCGCTA
63 TGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTA
42044147 AAGC
1 AAGC
42044151 CTTAAAAGGT
Statistics
Matches: 215, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
112 10 0.05
113 45 0.21
114 91 0.42
115 67 0.31
116 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (114 bp):
AAGCTCTGAGCATTAGCGGCGCTTTTTAAAAACTCCGCTAAAGCCCTGAAAGGTCAAAAAAATGA
TGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTA
Found at i:42044174 original size:187 final size:187
Alignment explanation
Indices: 42043933--42044324 Score: 583
Period size: 187 Copynumber: 2.1 Consensus size: 187
42043923 TTGAGCATTA
* * * * * *
42043933 GCGGCGCTTTTTCAAAAACT-CCACTAAAGCCCTGAAAGGTAAAAAAATGATGTCGTTGGGCTTA
1 GCGGCGCTTTTCCAAAAAATGTCGCTAAAGCCCTAAAAGGTAAAAAAACGATGTCGTTGGGCTTA
* *
42043997 GGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTTTTTAA
66 GGTTTTTTGCGACGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTTTTCAA
* * *
42044062 ATAA-GCTGCTAAAGCCCTGAAAGGTCAAAAAAATGATGTCGTTGGGCTTAGGTTTTTT
131 A-AATGCCGCTAAAGCACTGAAAGGTC-AAAAAACGATGTCGTTGGGCTTAGGTTTTTT
* * *
42044120 GCGGCGCTTTTCTAAAAAATGTCGCTAAAGCCTTAAAAGGT-CAAAAACGATGTCGTTGGGCTTA
1 GCGGCGCTTTTCCAAAAAATGTCGCTAAAGCCCTAAAAGGTAAAAAAACGATGTCGTTGGGCTTA
* * *
42044184 GGTTTTTTGCGACGCTTTTCCAAAAAGCGCCGGTAAAGCTTTGAGCATTAGCGGCGCTTTTTCAA
66 GGTTTTTTGCGACGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTTTTCAA
*
42044249 AAATGCCGTTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
131 AAATGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
42044306 GCGGCGCTTTTCCAAAAAA
1 GCGGCGCTTTTCCAAAAAA
42044325 CGCCACTAAA
Statistics
Matches: 184, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
186 50 0.27
187 118 0.64
188 16 0.09
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (187 bp):
GCGGCGCTTTTCCAAAAAATGTCGCTAAAGCCCTAAAAGGTAAAAAAACGATGTCGTTGGGCTTA
GGTTTTTTGCGACGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTTTTCAA
AAATGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
Found at i:42044183 original size:72 final size:72
Alignment explanation
Indices: 42044047--42044209 Score: 222
Period size: 72 Copynumber: 2.2 Consensus size: 72
42044037 CTGAGCATTA
* * * *
42044047 GCGGCGCTTTTTTAAATAAGCTGCTAAAGCCCTGAAAGGTCAAAAAAATGATGTCGTTGGGCTTA
1 GCGGCGCTTTTCTAAAAAAGCTGCTAAAGCCCTAAAAGGTC-AAAAAACGATGTCGTTGGGCTTA
42044112 GGTTTTTT
65 GGTTTTTT
*
42044120 GCGGCGCTTTTCTAAAAAATG-TCGCTAAAGCCTTAAAAGGTC-AAAAACGATGTCGTTGGGCTT
1 GCGGCGCTTTTCTAAAAAA-GCT-GCTAAAGCCCTAAAAGGTCAAAAAACGATGTCGTTGGGCTT
42044183 AGGTTTTTT
64 AGGTTTTTT
* *
42044192 GCGACGCTTTTCCAAAAA
1 GCGGCGCTTTTCTAAAAA
42044210 GCGCCGGTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
72 45 0.56
73 18 0.22
74 18 0.22
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (72 bp):
GCGGCGCTTTTCTAAAAAAGCTGCTAAAGCCCTAAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
GTTTTTT
Found at i:42044320 original size:114 final size:114
Alignment explanation
Indices: 42044120--42044455 Score: 487
Period size: 114 Copynumber: 2.9 Consensus size: 114
42044110 TAGGTTTTTT
* * *
42044120 GCGGCGCTTTTCTAAAAAATGTCGCTAAAGC-CTTAAAAGGTC-AAAAACGATGTCGTTGGGCTT
1 GCGGCGCTTTT-TCAAAAATGCCGCTAAAGCAC-TGAAAGGTCAAAAAACGATGTCGTTGGGCTT
* * * *
42044183 AGGTTTTTTGCGACGCTTTTCCAAAAAGCGCCGGTAAAGCTTTGAGCATTA
64 AGGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTA
*
42044234 GCGGCGCTTTTTCAAAAATGCCGTTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
*
42044299 GTTTTTTGCGGCGCTTTTCCAAAAAACGCCACTAAAGCTCTGAGCATTA
66 GTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTA
* * * *
42044348 GCGGCACTTTTTCAAAAACGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTTGTTGAGCTTAG
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
* ** *
42044413 GTTTTTTACGGCGCTTTTTTAAAAAACGCCGCTAAAGCCCTGA
66 GTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCTCTGA
42044456 AAGGTCAAAA
Statistics
Matches: 201, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
113 24 0.12
114 177 0.88
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (114 bp):
GCGGCGCTTTTTCAAAAATGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
GTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:42044385 original size:301 final size:299
Alignment explanation
Indices: 42043820--42044527 Score: 1091
Period size: 301 Copynumber: 2.4 Consensus size: 299
42043810 CTGAGAATTA
*
42043820 ACGGCGCTATTT-T-AAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAACAATGTCGTTGGGCTTA
1 ACGGCGCT-TTTCTAAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAACGATGTCGTTGGGCTTA
42043883 GGTTTTTTGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCTTTGAGCATTAGCGGCGCTTTTTCAA
65 GGTTTTTTGCGGCGCTTTTCC-AAAAACGCCGCTAAAGCTTTGAGCATTAGCGGCGCTTTTTCAA
* *
42043948 AAACTCCACTAAAGCCCTGAAAGGTAAAAAAATGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCT
129 AAACTCCACTAAAGCACTGAAAGGTAAAAAAACGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCT
* * * * *
42044013 TTTCCAAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTTTTTAAATAAGCTGCTAAAGCC
194 TTTCCAAAAAACGCCACTAAAGCTCTGAGCATTAGCGGCACTTTTTCAAATAAGCCGCTAAAGCA
* *
42044078 CTGAAAGGTCAAAAAAATGATGTCGTTGGGCTTAGGTTTTTT
259 CTGAAAGGTC-AAAAAACGATGTCGTTGAGCTTAGGTTTTTT
* * * * *
42044120 GCGGCGCTTTTCTAAAAAATGTCGCTAAAGCCTTAAAAGGTCAAAAACGATGTCGTTGGGCTTAG
1 ACGGCGCTTTTCTAAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAACGATGTCGTTGGGCTTAG
* *
42044185 GTTTTTTGCGACGCTTTTCCAAAAAGCGCCGGTAAAGCTTTGAGCATTAGCGGCGCTTTTTCAAA
66 GTTTTTTGCGGCGCTTTTCCAAAAA-CGCCGCTAAAGCTTTGAGCATTAGCGGCGCTTTTTCAAA
** *
42044250 AA-TGCCGTTAAAGCACTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCT
130 AACT-CCACTAAAGCACTGAAAGGTAAAAAAACGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCT
42044314 TTTCCAAAAAACGCCACTAAAGCTCTGAGCATTAGCGGCACTTTTTCAAA-AACGCCGCTAAAGC
194 TTTCCAAAAAACGCCACTAAAGCTCTGAGCATTAGCGGCACTTTTTCAAATAA-GCCGCTAAAGC
*
42044378 ACTGAAAGGTCAAAAAACGATGTTGTTGAGCTTAGGTTTTTT
258 ACTGAAAGGTCAAAAAACGATGTCGTTGAGCTTAGGTTTTTT
* *
42044420 ACGGCGCTTTTTTAAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAAATGATGTCGTTGGGCTTA
1 ACGGCGCTTTTCTAAAAAACGCCGCTAAAGCCCTGAAAGGTC-AAAAACGATGTCGTTGGGCTTA
* * *
42044485 GGTTTTTTGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTTGA
65 GGTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCTTTGA
42044528 AAGGTCAAAA
Statistics
Matches: 369, Mismatches: 33, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
299 3 0.01
300 94 0.25
301 272 0.74
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (299 bp):
ACGGCGCTTTTCTAAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAACGATGTCGTTGGGCTTAG
GTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCTTTGAGCATTAGCGGCGCTTTTTCAAAA
ACTCCACTAAAGCACTGAAAGGTAAAAAAACGATGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTT
TCCAAAAAACGCCACTAAAGCTCTGAGCATTAGCGGCACTTTTTCAAATAAGCCGCTAAAGCACT
GAAAGGTCAAAAAACGATGTCGTTGAGCTTAGGTTTTTT
Found at i:42044437 original size:72 final size:71
Alignment explanation
Indices: 42044348--42044577 Score: 352
Period size: 72 Copynumber: 3.2 Consensus size: 71
42044338 CTGAGCATTA
* * *
42044348 GCGGCACTTTTTCAAAAACGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTTGTTGAGCTTAG
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGC-CTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
42044413 GTTTTTT
65 GTTTTTT
* * *
42044420 ACGGCGCTTTTTTAAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAAATGATGTCGTTGGGCTTA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAG-CCTGAAAGGTCAAAAAACGATGTCGTTGGGCTTA
42044485 GGTTTTTT
64 GGTTTTTT
*
42044493 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCTTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCC-TGAAAGGTCAAAAAACGATGTCGTTGGGCTTAG
42044558 GTTTTTT
65 GTTTTTT
*
42044565 GCGACGCTTTTTC
1 GCGGCGCTTTTTC
42044578 TTTAGTGACG
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
71 2 0.01
72 76 0.53
73 65 0.45
74 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (71 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGG
TTTTTT
Found at i:42044439 original size:73 final size:72
Alignment explanation
Indices: 42044355--42044576 Score: 347
Period size: 73 Copynumber: 3.1 Consensus size: 72
42044345 TTAGCGGCAC
* *
42044355 TTTTTCAAAAACGCCGCTAAAGCACTGAAAGGTCAAAAAACGATGTTGTTGAGCTTAGGTTTTTT
1 TTTTTCAAAAACGCCGCTAAAGC-CTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
*
42044420 ACGGCGCT
65 GCGGCGCT
* *
42044428 TTTTTAAAAAACGCCGCTAAAGCCCTGAAAGGTCAAAAAATGATGTCGTTGGGCTTAGGTTTTTT
1 TTTTTCAAAAACGCCGCTAAAG-CCTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
42044493 GCGGCGC-
65 GCGGCGCT
*
42044500 TTTTTCAAAAATGCCGCTAAAGCCTTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
1 TTTTTCAAAAACGCCGCTAAAGCC-TGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTT
*
42044565 GCGACGCT
65 GCGGCGCT
42044573 TTTT
1 TTTT
42044577 CTTTAGTGAC
Statistics
Matches: 137, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
71 2 0.01
72 65 0.47
73 69 0.50
74 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (72 bp):
TTTTTCAAAAACGCCGCTAAAGCCTGAAAGGTCAAAAAACGATGTCGTTGGGCTTAGGTTTTTTG
CGGCGCT
Found at i:42046080 original size:43 final size:43
Alignment explanation
Indices: 42046023--42046232 Score: 201
Period size: 43 Copynumber: 4.9 Consensus size: 43
42046013 TTACGGAGAA
* *
42046023 AAACGCCGCAAAAGAACAAGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * * * *
42046066 AAACGTCGCGAAAGACCAAGACCTTTTGTGGCACTTCTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
42046109 AAACGCCGCTAAAG-ACTATGACCTTTAGCGGTGCTTTCCCCAC
1 AAACGCCGCTAAAGAAC-AAGACCTTTAGCGGCGCTTTTCCCAC
* ** *
42046152 AAACGCTGCTAAAGGCCAAGACCTTTAGCGGTGCTTTT-CCATC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCA-C
* * *
42046195 AAACGCCGCTAAA-AACCATGACCTTTAGTGGCGTTTTT
1 AAACGCCGCTAAAGAA-CAAGACCTTTAGCGGCGCTTTT
42046233 TTAAAAACGC
Statistics
Matches: 134, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
42 4 0.03
43 129 0.96
44 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:42046133 original size:86 final size:85
Alignment explanation
Indices: 42046023--42046222 Score: 224
Period size: 86 Copynumber: 2.3 Consensus size: 85
42046013 TTACGGAGAA
* * *
42046023 AAACGCCGCAAAAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACG-TCGCGAAAGACCAAGA
1 AAACGCCGCTAAAG-ACATGACCTTTAGCAGCGCTTTCCCCACAAACGCT-GCGAAAGACCAAGA
* *
42046087 CCTTTTGTGGCACTTCTCCCA-C
64 CCTTTAGCGGCACTT-TCCCATC
* * * *
42046109 AAACGCCGCTAAAGACTATGACCTTTAGCGGTGCTTTCCCCACAAACGCTGCTAAAGGCCAAGAC
1 AAACGCCGCTAAAGAC-ATGACCTTTAGCAGCGCTTTCCCCACAAACGCTGCGAAAGACCAAGAC
** *
42046174 CTTTAGCGGTGCTTTTCCATC
65 CTTTAGCGGCACTTTCCCATC
*
42046195 AAACGCCGCTAAAAACCATGACCTTTAG
1 AAACGCCGCTAAAGA-CATGACCTTTAG
42046223 TGGCGTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
85 6 0.06
86 89 0.92
87 2 0.02
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (85 bp):
AAACGCCGCTAAAGACATGACCTTTAGCAGCGCTTTCCCCACAAACGCTGCGAAAGACCAAGACC
TTTAGCGGCACTTTCCCATC
Found at i:42052144 original size:42 final size:41
Alignment explanation
Indices: 42052096--42052180 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
42052086 GTTGTTCACT
* *
42052096 TATATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATA
1 TATATTTAAAATTAAATAAATTATGTAAGTTATG-TATGATA
** * *
42052138 TATATTTATTATTAAGTAAATTATGTAAGTTATGTATTATA
1 TATATTTAAAATTAAATAAATTATGTAAGTTATGTATGATA
42052179 TA
1 TA
42052181 AGTTATTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 8 0.22
42 29 0.78
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (41 bp):
TATATTTAAAATTAAATAAATTATGTAAGTTATGTATGATA
Found at i:42052170 original size:9 final size:9
Alignment explanation
Indices: 42052153--42052295 Score: 79
Period size: 9 Copynumber: 16.7 Consensus size: 9
42052143 TTATTATTAA
*
42052153 GTAAATTAT
1 GTAAGTTAT
42052162 GTAAGTTAT
1 GTAAGTTAT
42052171 GT-A-TTAT
1 GTAAGTTAT
*
42052178 ATAAGTTAT
1 GTAAGTTAT
*
42052187 TTAAGTTAT
1 GTAAGTTAT
42052196 GT-A-TTAT
1 GTAAGTTAT
**
42052203 GTAACCTAT
1 GTAAGTTAT
42052212 GTAAGTTAT
1 GTAAGTTAT
**
42052221 GTAAGTGCT
1 GTAAGTTAT
42052230 GT-A-TTAT
1 GTAAGTTAT
**
42052237 GTAAGGCAAAT
1 GTAA-G-TTAT
42052248 -TAAGTTAT
1 GTAAGTTAT
* *
42052256 GTAGGCTAT
1 GTAAGTTAT
42052265 GT-A-TTAT
1 GTAAGTTAT
*
42052272 GCAAGTTAT
1 GTAAGTTAT
* *
42052281 TTAAGTTGT
1 GTAAGTTAT
42052290 GTAAGT
1 GTAAGT
42052296 GTTGTATTAT
Statistics
Matches: 99, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
7 19 0.19
8 9 0.09
9 66 0.67
10 3 0.03
11 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42052175 original size:25 final size:25
Alignment explanation
Indices: 42052143--42052223 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
42052133 TGATATATAT
42052143 TTAT-TATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* *
42052167 TTATGTATTATA-TAAGTTATTTAAG
1 TTATGTATTA-AGTAAATTATGTAAG
* **
42052192 TTATGTATTATGTAACCTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
42052217 TTATGTA
1 TTATGTA
42052224 AGTGCTGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
24 4 0.08
25 43 0.90
26 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:42052266 original size:69 final size:69
Alignment explanation
Indices: 42052179--42052333 Score: 220
Period size: 69 Copynumber: 2.2 Consensus size: 69
42052169 ATGTATTATA
* * * *
42052179 TAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGCAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
42052244 AAAT
66 AAAT
** * * *
42052248 TAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGCAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
42052313 AAAT
66 AAAT
*
42052317 TAAGTTATGTAGTCTAT
1 TAAGTTATGTAGGCTAT
42052334 CCCGCAACAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.43
Consensus pattern (69 bp):
TAAGTTATGTAGGCTATGTATTATGCAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
AAAT
Found at i:42052794 original size:9 final size:9
Alignment explanation
Indices: 42052777--42052919 Score: 79
Period size: 9 Copynumber: 16.7 Consensus size: 9
42052767 TATATATTAA
*
42052777 GTAAATTAT
1 GTAAGTTAT
42052786 GTAAGTTAT
1 GTAAGTTAT
42052795 GT-A-TTAT
1 GTAAGTTAT
*
42052802 ATAAGTTAT
1 GTAAGTTAT
*
42052811 TTAAGTTAT
1 GTAAGTTAT
42052820 GT-A-TTAT
1 GTAAGTTAT
**
42052827 GTAACCTAT
1 GTAAGTTAT
42052836 GTAAGTTAT
1 GTAAGTTAT
**
42052845 GTAAGTGCT
1 GTAAGTTAT
42052854 GT-A-TTAT
1 GTAAGTTAT
**
42052861 GTAAGGCAAAT
1 GTAA-G-TTAT
42052872 -TAAGTTAT
1 GTAAGTTAT
* *
42052880 GTAGGCTAT
1 GTAAGTTAT
42052889 GT-A-TTAT
1 GTAAGTTAT
*
42052896 GCAAGTTAT
1 GTAAGTTAT
* *
42052905 TTAAGTTGT
1 GTAAGTTAT
42052914 GTAAGT
1 GTAAGT
42052920 GTTGTATTAT
Statistics
Matches: 99, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
7 19 0.19
8 9 0.09
9 66 0.67
10 3 0.03
11 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42052794 original size:25 final size:25
Alignment explanation
Indices: 42052766--42052847 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
42052756 TGATATATAT
*
42052766 TTATATATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* *
42052791 TTATGTATTATA-TAAGTTATTTAAG
1 TTATGTATTA-AGTAAATTATGTAAG
* **
42052816 TTATGTATTATGTAACCTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
42052841 TTATGTA
1 TTATGTA
42052848 AGTGCTGTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:42052892 original size:69 final size:69
Alignment explanation
Indices: 42052803--42052957 Score: 220
Period size: 69 Copynumber: 2.2 Consensus size: 69
42052793 ATGTATTATA
* * * *
42052803 TAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGCAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
42052868 AAAT
66 AAAT
** * * *
42052872 TAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGCAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
42052937 AAAT
66 AAAT
*
42052941 TAAGTTATGTAGTCTAT
1 TAAGTTATGTAGGCTAT
42052958 CCTGCAACAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.43
Consensus pattern (69 bp):
TAAGTTATGTAGGCTATGTATTATGCAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
AAAT
Found at i:42053104 original size:624 final size:623
Alignment explanation
Indices: 42051709--42053581 Score: 3611
Period size: 624 Copynumber: 3.0 Consensus size: 623
42051699 ATATTAATGC
42051709 ATCCCGCAACATACCTTCCATGTCATCCCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
1 ATCCCGCAACATACCTTCCATGTCATCCCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
42051774 ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
66 ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
* * * *
42051839 CCCCAAACAAAACCATCAATAATTAGATGCTCGTATACAACTTCACGATAATGCTATTTTATTTT
131 CCCCAAACAAAACCATCAACAATTAGATGCTCGTATACAACTTCACGATAATGCCAGTTTATGTT
42051904 GACACACTTGTTACAGGGGCAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
196 GACACACTTGTTACAGGGGCAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
42051969 GAAAACTCTGAACTCCATTTCAATAATTGTTGCTTACCCTTGACAAATTCATCCAAGACTGGTCT
261 GAAAACTCTGAACTCCATTTCAATAATTGTTGCTTACCCTTGACAAATTCATCCAAGACTGGTCT
42052034 ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACGTAAGTTGTTCACTTAT
326 ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACGTAAGTTGTTCACTTAT
42052099 ATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATATATATTTATTATTAAGTAAATTATGT
391 ATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATATATATTTATTATTAAGTAAATTATGT
42052164 AAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTGC
456 AAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTGC
42052229 TGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAA
521 TGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAA
42052294 GTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
586 GTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
* *
42052332 ATCCCGCAACATACCTTTCATGTCATCTCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
1 ATCCCGCAACATACCTTCCATGTCATCCCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
42052397 ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
66 ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
42052462 CCCCAAACAAAACCATCAACAATTAGATGCTCGTATACAACTTCACGATAATGCCAGTTTATGTT
131 CCCCAAACAAAACCATCAACAATTAGATGCTCGTATACAACTTCACGATAATGCCAGTTTATGTT
42052527 GACACACTTGTTACAGGGGCAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
196 GACACACTTGTTACAGGGGCAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
42052592 GAAAACTCTGAACTCCATTTCAATAATTGTTGCTTACCCTTGACAAATTCATCCAAGACTGGTCT
261 GAAAACTCTGAACTCCATTTCAATAATTGTTGCTTACCCTTGACAAATTCATCCAAGACTGGTCT
42052657 ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACGTAAGTTGTTCACTTAT
326 ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACGTAAGTTGTTCACTTAT
42052722 ATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATATATATTTATATATTAAGTAAATTATG
391 ATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATATATATTTAT-TATTAAGTAAATTATG
42052787 TAAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTG
455 TAAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTG
42052852 CTGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTA
520 CTGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTA
42052917 AGTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
585 AGTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
*
42052956 ATCCTGCAACATACCTTCCATGTCATCCCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
1 ATCCCGCAACATACCTTCCATGTCATCCCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
42053021 ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
66 ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
*
42053086 CCCCAAACAAACCCATCAACAATTAGATGCTCGTATACAACTTCACGATAATGCCAGTTTATGTT
131 CCCCAAACAAAACCATCAACAATTAGATGCTCGTATACAACTTCACGATAATGCCAGTTTATGTT
*
42053151 GACACACTTGTTACAGGGGTAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
196 GACACACTTGTTACAGGGGCAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
* *
42053216 GAAAACTCTGAACTCCATTTCAATAACTGTTGCTTACCCTTGACAAATTCATCCAAGACCGGTCT
261 GAAAACTCTGAACTCCATTTCAATAATTGTTGCTTACCCTTGACAAATTCATCCAAGACTGGTCT
*
42053281 ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACATAAGTTGTTCACTTAT
326 ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACGTAAGTTGTTCACTTAT
*
42053346 ATTTAAAATTAAATGAGTTATGTAAGTTATGATATAATATATATTTATGTATTAAGTAAATTATG
391 ATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATATATATTTAT-TATTAAGTAAATTATG
42053411 TAAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTG
455 TAAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTG
42053476 CTGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTA
520 CTGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTA
42053541 AGTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
585 AGTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
42053580 AT
1 AT
42053582 GTATTATGGA
Statistics
Matches: 1233, Mismatches: 16, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
623 432 0.35
624 801 0.65
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (623 bp):
ATCCCGCAACATACCTTCCATGTCATCCCCTCCAACAGACTGATAGTAAGCAGTACCAGGATAAG
ATACATCCATCGTTGAAGAGGAGGTACTAGGCGGGCATTCTCCATGAAAAAGCCATTTTTTATAA
CCCCAAACAAAACCATCAACAATTAGATGCTCGTATACAACTTCACGATAATGCCAGTTTATGTT
GACACACTTGTTACAGGGGCAAAGAATCATGTTCTCTTGGCTTGCATGTTGAAATGAAAAATTTA
GAAAACTCTGAACTCCATTTCAATAATTGTTGCTTACCCTTGACAAATTCATCCAAGACTGGTCT
ATTTCTTAATTCTTGAAGTCTGATTTCCACCAGAAAATACAAGGGTACGTAAGTTGTTCACTTAT
ATTTAAAATTAAATGAGTTATGTAAGTTATGATATGATATATATTTATTATTAAGTAAATTATGT
AAGTTATGTATTATATAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTGC
TGTATTATGTAAGGCAAATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAA
GTGTTGTATTATGTAAGGCAAATTAAGTTATGTAGTCT
Found at i:42053418 original size:9 final size:9
Alignment explanation
Indices: 42053401--42054109 Score: 202
Period size: 9 Copynumber: 81.6 Consensus size: 9
42053391 TATGTATTAA
*
42053401 GTAAATTAT
1 GTAAGTTAT
42053410 GTAAGTTAT
1 GTAAGTTAT
42053419 GT-A-TTAT
1 GTAAGTTAT
*
42053426 ATAAGTTAT
1 GTAAGTTAT
*
42053435 TTAAGTTAT
1 GTAAGTTAT
42053444 GT-A-TTAT
1 GTAAGTTAT
**
42053451 GTAACCTAT
1 GTAAGTTAT
42053460 GTAAGTTAT
1 GTAAGTTAT
**
42053469 GTAAGTGCT
1 GTAAGTTAT
42053478 GT-A-TTAT
1 GTAAGTTAT
**
42053485 GTAAGGCAAAT
1 GTAA-G-TTAT
42053496 -TAAGTTAT
1 GTAAGTTAT
* *
42053504 GTAGGCTAT
1 GTAAGTTAT
42053513 GT-A-TTAT
1 GTAAGTTAT
*
42053520 GCAAGTTAT
1 GTAAGTTAT
* *
42053529 TTAAGTTGT
1 GTAAGTTAT
42053538 GTAAGTGT-T
1 GTAAGT-TAT
42053547 GT-A-TTAT
1 GTAAGTTAT
**
42053554 GTAAGGCAAAT
1 GTAA-G-TTAT
42053565 -TAAGTTAT
1 GTAAGTTAT
42053573 GT-AGTCTAT
1 GTAAGT-TAT
42053582 GT-A-TTAT
1 GTAAGTTAT
*
42053589 GGAAGTTAT
1 GTAAGTTAT
* *
42053598 TTAAGTTGT
1 GTAAGTTAT
42053607 GTAAGTGT-T
1 GTAAGT-TAT
42053616 GT-A-TTAT
1 GTAAGTTAT
**
42053623 GTAAGGCAAAT
1 GTAA-G-TTAT
42053634 -TAAGTTAT
1 GTAAGTTAT
42053642 GT-AGTCTAT
1 GTAAGT-TAT
42053651 GT-A-TTAT
1 GTAAGTTAT
*
42053658 GGAAGTTAT
1 GTAAGTTAT
* *
42053667 TTAAGTTGT
1 GTAAGTTAT
42053676 GTAAGTGT-T
1 GTAAGT-TAT
*
42053685 GTATTA-TGTAA
1 GTA--AGT-TAT
42053696 GTAAGTTAT
1 GTAAGTTAT
42053705 GT-A-TTAT
1 GTAAGTTAT
42053712 GTAAGTTTTAT
1 GTAAG--TTAT
**
42053723 GTAAAATAT
1 GTAAGTTAT
42053732 GTAAG-T-T
1 GTAAGTTAT
**
42053739 GTATTTTAT
1 GTAAGTTAT
*
42053748 GAAAGTTAT
1 GTAAGTTAT
*
42053757 ATAAGTTAT
1 GTAAGTTAT
* *
42053766 GTAGGCTAT
1 GTAAGTTAT
*
42053775 GT--TTTAT
1 GTAAGTTAT
*
42053782 GCAAGTTAT
1 GTAAGTTAT
* * *
42053791 TTAATTTCT
1 GTAAGTTAT
42053800 GTAAGTGT-T
1 GTAAGT-TAT
42053809 GT-A-TTAT
1 GTAAGTTAT
*
42053816 ATAAGTTAT
1 GTAAGTTAT
42053825 GT-A-TTAT
1 GTAAGTTAT
*
42053832 GTAAGATAT
1 GTAAGTTAT
42053841 GTAAG-T-T
1 GTAAGTTAT
**
42053848 GTATTTTAT
1 GTAAGTTAT
42053857 GTAAGTTAT
1 GTAAGTTAT
42053866 GT-A-TTAT
1 GTAAGTTAT
*
42053873 GTATGTTAT
1 GTAAGTTAT
*
42053882 GTAAGTAAT
1 GTAAGTTAT
42053891 G--AGTTAT
1 GTAAGTTAT
*
42053898 GTAAGCTAT
1 GTAAGTTAT
42053907 GTAAGTTAT
1 GTAAGTTAT
42053916 GTAAGTTAT
1 GTAAGTTAT
*
42053925 TTAAGTGGTGTAT
1 GTAA---GT-TAT
42053938 -TAAGTTAT
1 GTAAGTTAT
*
42053946 GGAAGTTAATAT
1 GTAAG-T--TAT
42053958 GTAAGTTAT
1 GTAAGTTAT
*
42053967 GCAAGCTTATAT
1 GTAAG--T-TAT
*
42053979 ATAAGTTAT
1 GTAAGTTAT
42053988 GT-A-TTAT
1 GTAAGTTAT
*
42053995 GTTA-TTAT
1 GTAAGTTAT
42054003 GT-A-TTAT
1 GTAAGTTAT
*
42054010 GTAATTTAT
1 GTAAGTTAT
*
42054019 -TATGTTAT
1 GTAAGTTAT
42054027 -T-A--TAT
1 GTAAGTTAT
*
42054032 ATAAGTTAT
1 GTAAGTTAT
*
42054041 GGAAGTTATTAT
1 GTAAG---TTAT
42054053 GTAAGTTAT
1 GTAAGTTAT
*
42054062 GCAAGCTTATAT
1 GTAAG--T-TAT
*
42054074 ATAAGTTAT
1 GTAAGTTAT
42054083 GT-A-TTAT
1 GTAAGTTAT
*
42054090 GTTA-TTAT
1 GTAAGTTAT
42054098 GT-A-TTAT
1 GTAAGTTAT
42054105 GTAAG
1 GTAAG
42054110 CAAATGATTG
Statistics
Matches: 520, Mismatches: 97, Indels: 166
0.66 0.12 0.21
Matches are distributed among these distances:
5 3 0.01
6 4 0.01
7 101 0.19
8 66 0.13
9 270 0.52
10 20 0.04
11 21 0.04
12 32 0.06
13 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42053534 original size:69 final size:69
Alignment explanation
Indices: 42053427--42053696 Score: 432
Period size: 69 Copynumber: 3.9 Consensus size: 69
42053417 ATGTATTATA
* * * * ** * * *
42053427 TAAGTTATTTAAGTTATGTATTATGTAACCTATGTAAGTTATGTAAGTGCTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
42053492 AAAT
66 AAAT
*
42053496 TAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
42053561 AAAT
66 AAAT
*
42053565 TAAGTTATGTAGTCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
1 TAAGTTATGTAGGCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
42053630 AAAT
66 AAAT
*
42053634 TAAGTTATGTAGTCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAG
1 TAAGTTATGTAGGCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAG
42053697 TAAGTTATGT
Statistics
Matches: 190, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 190 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (69 bp):
TAAGTTATGTAGGCTATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAAGGC
AAAT
Found at i:42053550 original size:34 final size:34
Alignment explanation
Indices: 42053443--42053697 Score: 221
Period size: 34 Copynumber: 7.4 Consensus size: 34
42053433 ATTTAAGTTA
** * * *
42053443 TGTATTATGTAACCTATGTAAGTTATGTAAGTGC
1 TGTATTATGTAAGTTATTTAAGTTGTGTAAGTGT
** * *
42053477 TGTATTATGTAAGGCAAATTAAGTTATGT-AG-GCT
1 TGTATTATGTAA-GTTATTTAAGTTGTGTAAGTG-T
*
42053511 ATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGT
1 -TGTATTATGTAAGTTATTTAAGTTGTGTAAGTGT
** * * *
42053546 TGTATTATGTAAGGCAAATTAAGTTATGT-AGTCT
1 TGTATTATGTAA-GTTATTTAAGTTGTGTAAGTGT
*
42053580 ATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGT
1 -TGTATTATGTAAGTTATTTAAGTTGTGTAAGTGT
** * * *
42053615 TGTATTATGTAAGGCAAATTAAGTTATGT-AGTCT
1 TGTATTATGTAA-GTTATTTAAGTTGTGTAAGTGT
*
42053649 ATGTATTATGGAAGTTATTTAAGTTGTGTAAGTGT
1 -TGTATTATGTAAGTTATTTAAGTTGTGTAAGTGT
42053684 TGTATTATGTAAGT
1 TGTATTATGTAAGT
42053698 AAGTTATGTA
Statistics
Matches: 175, Mismatches: 35, Indels: 22
0.75 0.15 0.09
Matches are distributed among these distances:
33 1 0.01
34 93 0.53
35 80 0.46
36 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (34 bp):
TGTATTATGTAAGTTATTTAAGTTGTGTAAGTGT
Found at i:42053767 original size:34 final size:34
Alignment explanation
Indices: 42053729--42053865 Score: 87
Period size: 34 Copynumber: 3.8 Consensus size: 34
42053719 TTATGTAAAA
42053729 TATGTAAGTTGTATTTTATGAAAGTTATATAAGT
1 TATGTAAGTTGTATTTTATGAAAGTTATATAAGT
* * * * * * *
42053763 TATGTAGGCTATGTTTTATGCAAGTTATTTAATT
1 TATGTAAGTTGTATTTTATGAAAGTTATATAAGT
* * * *
42053797 TCTGTAAGTGTTGTATTATAT-AAGTTATGTATTATGTAAGA
1 TATGTAA--GTTGTATTTTATGAA---A-G--TTATATAAGT
*
42053838 TATGTAAGTTGTATTTTATGTAAGTTAT
1 TATGTAAGTTGTATTTTATGAAAGTTAT
42053866 GTATTATGTA
Statistics
Matches: 74, Mismatches: 20, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
34 36 0.49
35 1 0.01
36 9 0.12
37 1 0.01
38 1 0.01
39 12 0.16
40 1 0.01
41 13 0.18
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (34 bp):
TATGTAAGTTGTATTTTATGAAAGTTATATAAGT
Found at i:42053845 original size:25 final size:26
Alignment explanation
Indices: 42053361--42053930 Score: 123
Period size: 25 Copynumber: 22.5 Consensus size: 26
42053351 AAATTAAATG
* *
42053361 AGTTATGTAAGTTATGATATA-ATATAT
1 AGTTATGTAAGTTATG-TA-AGTTATGT
* * *
42053388 ATTTATGT-A-TTAAGTAAATTATGT
1 AGTTATGTAAGTTATGTAAGTTATGT
* *
42053412 AAGTTATGT-A-TTATATAAGTTATTT
1 -AGTTATGTAAGTTATGTAAGTTATGT
**
42053437 AAGTTATGT-A-TTATGTAACCTATGT
1 -AGTTATGTAAGTTATGTAAGTTATGT
**
42053462 AAGTTATGTAAGTGCTGT-A-TTATGT
1 -AGTTATGTAAGTTATGTAAGTTATGT
** * *
42053487 AAGGCAAAT-TAAGTTATGTAGGCTATGT
1 -A-G-TTATGTAAGTTATGTAAGTTATGT
* * *
42053515 A-TTATGCAAGTTATTTAAGTTGTGT
1 AGTTATGTAAGTTATGTAAGTTATGT
**
42053540 AAGTGT-TGT-A-TTATGTAAGGCAAAT-T
1 -AGT-TATGTAAGTTATGTAA-G-TTATGT
*
42053566 AAGTTATGT-AGTCTATGT-A-TTATGGA
1 -AGTTATGTAAGT-TATGTAAGTTAT-GT
* *
42053592 AGTTATTTAAGTTGTGTAAGTGT-TGT
1 AGTTATGTAAGTTATGTAAGT-TATGT
**
42053618 A-TTATGTAAGGCAAAT-TAAGTTATGT
1 AGTTATGTAA-G-TTATGTAAGTTATGT
* *
42053644 AGTCTATGT-A-TTATGGAAGTTATTT
1 AGT-TATGTAAGTTATGTAAGTTATGT
*
42053669 AAGTTGTGTAAGTGT-TGT-A-TTATGT
1 -AGTTATGTAAGT-TATGTAAGTTATGT
42053694 A---A-GTAAGTTATGT-A-TTATGT
1 AGTTATGTAAGTTATGTAAGTTATGT
**
42053714 AAGTTTTATGTAAAATATGTAAG-T-TGT
1 -AG--TTATGTAAGTTATGTAAGTTATGT
* * *
42053741 ATTTTATGAAAGTTATATAAGTTATGT
1 A-GTTATGTAAGTTATGTAAGTTATGT
* * * *
42053768 AGGCTATGT--TTTATGCAAGTTATTT
1 A-GTTATGTAAGTTATGTAAGTTATGT
* * *
42053793 AATTTCTGTAAGTGT-TGT-A-TTATAT
1 -AGTTATGTAAGT-TATGTAAGTTATGT
*
42053818 AAGTTATGT-A-TTATGTAAGATATGT
1 -AGTTATGTAAGTTATGTAAGTTATGT
**
42053843 AAG-T-TGTATTTTATGTAAGTTATGT
1 -AGTTATGTAAGTTATGTAAGTTATGT
* *
42053868 A-TTATGTATGTTATGTAAGTAATG-
1 AGTTATGTAAGTTATGTAAGTTATGT
*
42053892 AGTTATGTAAGCTATGTAAGTTATGT
1 AGTTATGTAAGTTATGTAAGTTATGT
*
42053918 AAGTTATTTAAGT
1 -AGTTATGTAAGT
42053931 GGTGTATTAA
Statistics
Matches: 397, Mismatches: 86, Indels: 120
0.66 0.14 0.20
Matches are distributed among these distances:
19 1 0.00
20 16 0.04
21 1 0.00
22 1 0.00
23 8 0.02
24 19 0.05
25 219 0.55
26 50 0.13
27 61 0.15
28 21 0.05
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (26 bp):
AGTTATGTAAGTTATGTAAGTTATGT
Found at i:42053962 original size:21 final size:21
Alignment explanation
Indices: 42053938--42053988 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
42053928 AGTGGTGTAT
* *
42053938 TAAGTTATGGAAG-TTAATATG
1 TAAGTTATGCAAGCTT-ATATA
42053959 TAAGTTATGCAAGCTTATATA
1 TAAGTTATGCAAGCTTATATA
42053980 TAAGTTATG
1 TAAGTTATG
42053989 TATTATGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (21 bp):
TAAGTTATGCAAGCTTATATA
Found at i:42054002 original size:8 final size:7
Alignment explanation
Indices: 42053984--42054029 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
42053974 TATATATAAG
42053984 TTATGTA
1 TTATGTA
42053991 TTATGTTA
1 TTATG-TA
42053999 TTATGTA
1 TTATGTA
42054006 TTATGTA
1 TTATGTA
*
42054013 --ATTTA
1 TTATGTA
42054018 TTATGTTA
1 TTATG-TA
42054026 TTAT
1 TTAT
42054030 ATATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:42054004 original size:15 final size:15
Alignment explanation
Indices: 42053984--42054106 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 15
42053974 TATATATAAG
42053984 TTATGTATTATGTTA
1 TTATGTATTATGTTA
42053999 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
42054013 --ATTTATTATGTTA
1 TTATGTATTATGTTA
* *
42054026 TTATATA-TAAGTTA
1 TTATGTATTATGTTA
* * *
42054040 TGGAAGTTATTATGTAA
1 T-TATG-TATTATGTTA
* *
42054057 GTTATGCAAGCTTATATATAA
1 -TTATG-TA--TTATGT-T-A
42054078 GTTATGTATTATGTTA
1 -TTATGTATTATGTTA
42054094 TTATGTATTATGT
1 TTATGTATTATGT
42054107 AAGCAAATGA
Statistics
Matches: 81, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
12 9 0.11
13 2 0.02
14 9 0.11
15 30 0.37
16 3 0.04
17 9 0.11
18 6 0.07
19 5 0.06
20 1 0.01
21 7 0.09
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.52
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:42054059 original size:21 final size:21
Alignment explanation
Indices: 42054026--42054083 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
42054016 TATTATGTTA
*
42054026 TTATATATAAGTTATGGAAG-
1 TTATATATAAGTTATGCAAGC
*
42054046 TTATTATGTAAGTTATGCAAGC
1 TTA-TATATAAGTTATGCAAGC
42054068 TTATATATAAGTTATG
1 TTATATATAAGTTATG
42054084 TATTATGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (21 bp):
TTATATATAAGTTATGCAAGC
Found at i:42054332 original size:61 final size:61
Alignment explanation
Indices: 42054252--42054393 Score: 194
Period size: 61 Copynumber: 2.3 Consensus size: 61
42054242 AAAAATATAT
* * * * *
42054252 AATTATTTAGAAAAATTATAAAATTGATACTTATAAATTTTATTAATAATAAATTTAGAAC
1 AATTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATAATAATAAATTTAGAAA
* * * * *
42054313 ACTTTTTTAGAATACTTATAAATTTAATACTAATAAATTTTAATACTAATAAATTTAGAAA
1 AATTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATAATAATAAATTTAGAAA
42054374 AATTATTTAGAAAACTTATA
1 AATTATTTAGAAAACTTATA
42054394 TAGAAAATAA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (61 bp):
AATTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATAATAATAAATTTAGAAA
Found at i:42054343 original size:15 final size:15
Alignment explanation
Indices: 42054323--42054369 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
42054313 ACTTTTTTAG
*
42054323 AATACTTATAAATTT
1 AATACTAATAAATTT
42054338 AATACTAATAAATTTT
1 AATACTAATAAA-TTT
42054354 AATACTAATAAATTT
1 AATACTAATAAATTT
42054369 A
1 A
42054370 GAAAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
AATACTAATAAATTT
Done.