Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 20 of 64
Found at i:2827348 original size:13 final size:13
Alignment explanation
Indices: 2827330--2827354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2827320 CATTGGAGAA
2827330 TGAATTTTTTGAT
1 TGAATTTTTTGAT
2827343 TGAATTTTTTGA
1 TGAATTTTTTGA
2827355 CGAGGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
TGAATTTTTTGAT
Found at i:2827961 original size:18 final size:17
Alignment explanation
Indices: 2827938--2827991 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2827928 TAATAACAAG
2827938 AAAATCCTTTCAATAAAA
1 AAAATCCTTTCAA-AAAA
* * *
2827956 AAAATCTTTTTAAAATA
1 AAAATCCTTTCAAAAAA
* *
2827973 AAAATCCCTACAAAAAA
1 AAAATCCTTTCAAAAAA
2827990 AA
1 AA
2827992 TTCATGAATT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATCCTTTCAAAAAA
Found at i:2831073 original size:33 final size:29
Alignment explanation
Indices: 2831032--2831110 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 29
2831022 AAGAGAAATG
2831032 AAAAAAAAATAAAAAAAATGTGTGTAAAAAAC
1 AAAAAAAAATAAAAAAAAT-T-TGT-AAAAAC
2831064 AACAAAAAAA-ACAAAAAAATTTGTAAAAAC
1 AA-AAAAAAATA-AAAAAAATTTGTAAAAAC
*
2831094 AAAAAAGAAGTAAAAAA
1 AAAAAA-AAATAAAAAA
2831111 GAAAAAAGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
29 4 0.10
30 15 0.36
31 4 0.10
32 4 0.10
33 15 0.36
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.13
Consensus pattern (29 bp):
AAAAAAAAATAAAAAAAATTTGTAAAAAC
Found at i:2831134 original size:18 final size:18
Alignment explanation
Indices: 2831088--2831128 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2831078 AAAAATTTGT
*
2831088 AAAAACAAAAAAGAAGTA
1 AAAAAGAAAAAAGAAGTA
2831106 AAAAAGAAAAAAG-AG-A
1 AAAAAGAAAAAAGAAGTA
2831122 AAAAAGA
1 AAAAAGA
2831129 GGAAAAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAGAAGTA
Found at i:2832554 original size:86 final size:85
Alignment explanation
Indices: 2832435--2832771 Score: 399
Period size: 86 Copynumber: 3.9 Consensus size: 85
2832425 TCTGAAAGTC
*
2832435 CTTGCAT-TTTGTGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATG
1 CTTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATG
2832499 AATCTGAAAGTCCTTGTGAA
66 AATCTGAAAGTCCTTGTGAA
* * * * * *
2832519 CTTTGCATCTTTACGAATCTAGAACCTTTGTGAAACTT-AGAATTTTGTGAATATTTCTTTCTTG
1 C-TTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGA-AATCTTATGAATCTTTCTTTCTTA
** * *
2832583 CAAATCTAAAAGTCTTTGTGAA
64 TGAATCTGAAAGTCCTTGTGAA
* * * * * *
2832605 CCTTGCATCTTTGCAAATCTAGAACCTTTGTGAAACTTGAAATCTTGTAAATCTTTTTTTTTTAT
1 -CTTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTAT
* **
2832670 GAATCTGAAAGTCTTTGCAAA
65 GAATCTGAAAGTCCTTGTGAA
* * * * *
2832691 CTTGAAATCTTTGCGAATCTAGAACCTTTGCGAAGCTTGAAATCTTACGAATCTTTCTTTCCTGT
1 CTTG-CATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTAT
2832756 GAATCTGAAAGTCCTT
65 GAATCTGAAAGTCCTT
2832772 ACGAACCTGA
Statistics
Matches: 211, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.00
85 11 0.05
86 197 0.93
87 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (85 bp):
CTTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATG
AATCTGAAAGTCCTTGTGAA
Found at i:2832657 original size:34 final size:34
Alignment explanation
Indices: 2832578--2832658 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
2832568 AATATTTCTT
* * *
2832578 TCTTGCAAATCTAAAAGTCTTTGTGAACCTTGCA
1 TCTTGCAAATCTAAAAGCCTTTGTGAAACTTGAA
*
2832612 TCTTTGCAAATCTAGAA-CCTTTGTGAAACTTGAAA
1 TC-TTGCAAATCTAAAAGCCTTTGTGAAACTTG-AA
*
2832647 TCTTGTAAATCT
1 TCTTGCAAATCT
2832659 TTTTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 24 0.60
35 16 0.40
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (34 bp):
TCTTGCAAATCTAAAAGCCTTTGTGAAACTTGAA
Found at i:2832703 original size:17 final size:18
Alignment explanation
Indices: 2832675--2832736 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
2832665 TTTATGAATC
2832675 TGAAAGTCTTTGC-AAACT
1 TGAAA-TCTTTGCGAAACT
*
2832693 TGAAATCTTTGCGAATCT
1 TGAAATCTTTGCGAAACT
* * *
2832711 AG-AACCTTTGCGAAGCT
1 TGAAATCTTTGCGAAACT
2832728 TGAAATCTT
1 TGAAATCTT
2832737 ACGAATCTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (18 bp):
TGAAATCTTTGCGAAACT
Found at i:2832783 original size:86 final size:85
Alignment explanation
Indices: 2832442--2832820 Score: 375
Period size: 86 Copynumber: 4.4 Consensus size: 85
2832432 GTCCTTGCAT
*
2832442 TTTGTGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
* * *
2832507 AGTCCTTGTGAACTTTGCATC
66 AGTCCTTGCGAAC-CTGAATC
* * * * * *** *
2832528 TTTACGAATCTAGAACCTTTGTGAAACTT-AGAATTTTGTGAATATTTCTTTCTTGCAAATCTAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGA-AATCTTATGAATCTTTCTTTCTTATGAATCTGA
* * *
2832592 AAGTCTTTGTGAACCTTGCATC
65 AAGTCCTTGCGAACC-TGAATC
* * * * * *
2832614 TTTGCAAATCTAGAACCTTTGTGAAACTTGAAATCTTGTAAATCTTTTTTTTTTATGAATCTGAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
* * *
2832679 AGTCTTTGCAAACTTGAAATC
66 AGTCCTTGCGAACCTG-AATC
* * * *
2832700 TTTGCGAATCTAGAACCTTTGCGAAGCTTGAAATCTTACGAATCTTTCTTTCCTGTGAATCTGAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
* *
2832765 AGTCCTTACGAACCTGAAACC
66 AGTCCTTGCGAACCTG-AATC
* * * *
2832786 TTTACGAATTTGAAAACCTTTGCGAATCTT-AAATC
1 TTTGCGAATCT-AGAACCTTTGCGAAACTTGAAATC
2832821 CTTGTTAAAA
Statistics
Matches: 242, Mismatches: 46, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
85 3 0.01
86 222 0.92
87 17 0.07
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (85 bp):
TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
AGTCCTTGCGAACCTGAATC
Found at i:2836914 original size:11 final size:11
Alignment explanation
Indices: 2836898--2836937 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2836888 CAATCTTTTG
2836898 TCTATTAGTTT
1 TCTATTAGTTT
*
2836909 TCTATTGGTTT
1 TCTATTAGTTT
2836920 TCTATTAAGTTT
1 TCTATT-AGTTT
2836932 T-TATTA
1 TCTATTA
2836938 TTCTCAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 1 0.04
11 20 0.77
12 5 0.19
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.62
Consensus pattern (11 bp):
TCTATTAGTTT
Found at i:2837178 original size:19 final size:20
Alignment explanation
Indices: 2837156--2837195 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2837146 ATGTAATTCA
*
2837156 ATTTTAAGTTTAAGTT-ATT
1 ATTTTAAGATTAAGTTGATT
*
2837175 ATTTTGAGATTAAGTTGATT
1 ATTTTAAGATTAAGTTGATT
2837195 A
1 A
2837196 GACTGCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (20 bp):
ATTTTAAGATTAAGTTGATT
Found at i:2840247 original size:22 final size:21
Alignment explanation
Indices: 2840222--2840267 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
2840212 AAAAAAAAAA
*
2840222 AAAAAACTTTTTAATGTAATAG
1 AAAAAACTATTTAAT-TAATAG
*
2840244 AAAAAACTATTTAATTATTAG
1 AAAAAACTATTTAATTAATAG
2840265 AAA
1 AAA
2840268 CGTGTTGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAAACTATTTAATTAATAG
Found at i:2841093 original size:14 final size:14
Alignment explanation
Indices: 2841067--2841122 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
2841057 AATACAGCAT
2841067 AATTTTT-AGAAATA
1 AATTTTTGA-AAATA
2841081 AATTTTTGAAAATCTA
1 AATTTTTGAAAA--TA
* * *
2841097 TATTCTAGAAAATA
1 AATTTTTGAAAATA
2841111 AATTTTTGAAAA
1 AATTTTTGAAAA
2841123 CTTAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 21 0.64
15 1 0.03
16 11 0.33
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (14 bp):
AATTTTTGAAAATA
Found at i:2841578 original size:16 final size:17
Alignment explanation
Indices: 2841557--2841592 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2841547 AATGTTATAA
2841557 TTAAAAATAAT-AAAAT
1 TTAAAAATAATAAAAAT
*
2841573 TTAAAATTAATAAAAAT
1 TTAAAAATAATAAAAAT
2841590 TTA
1 TTA
2841593 CTTTTACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATAATAAAAAT
Found at i:2841961 original size:20 final size:20
Alignment explanation
Indices: 2841936--2841976 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2841926 TTTAATTTAA
* *
2841936 TTTAAAACTATTATAAAATT
1 TTTAAAACTAATAAAAAATT
*
2841956 TTTAAAATTAATAAAAAATT
1 TTTAAAACTAATAAAAAATT
2841976 T
1 T
2841977 ATTATATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAACTAATAAAAAATT
Found at i:2843892 original size:24 final size:24
Alignment explanation
Indices: 2843864--2843912 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2843854 TATAAGCTAA
2843864 AAAAACTACTATCTTATATTGCAAT
1 AAAAA-TACTATCTTATATTGCAAT
* *
2843889 AAAAATATTATTTTATATTGCAAT
1 AAAAATACTATCTTATATTGCAAT
2843913 TGTCCAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (24 bp):
AAAAATACTATCTTATATTGCAAT
Found at i:2844859 original size:17 final size:17
Alignment explanation
Indices: 2844838--2844869 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2844828 AAGCTAATTT
2844838 TTTTTTA-TTATTTTTC
1 TTTTTTATTTATTTTTC
2844854 TTTTTTATTTATTTTT
1 TTTTTTATTTATTTTT
2844870 TCTAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTATTTATTTTTC
Found at i:2847819 original size:15 final size:14
Alignment explanation
Indices: 2847799--2847834 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2847789 TTTTTATATG
2847799 CATGCATTCATGCAT
1 CATGCATTCATGC-T
*
2847814 CATGCATTCATTCT
1 CATGCATTCATGCT
2847828 CATGCAT
1 CATGCAT
2847835 AATCTGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (14 bp):
CATGCATTCATGCT
Found at i:2851633 original size:51 final size:51
Alignment explanation
Indices: 2851577--2851676 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
2851567 TTGTATCTTT
* * *
2851577 GCAAATCT-AAAACCTTTGCAAAACTTGGAATCTTGCGAATCTTTCTTTCCC
1 GCAAATCTGAAAACCTTTAC-AAACTTGAAATCTTACGAATCTTTCTTTCCC
* ** *
2851628 GCAAATTTGAAAGTCTTTACAAACTTGAAATCTTATGAATCTTTCTTTC
1 GCAAATCTGAAAACCTTTACAAACTTGAAATCTTACGAATCTTTCTTTC
2851677 TTGTGAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 33 0.80
52 8 0.20
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (51 bp):
GCAAATCTGAAAACCTTTACAAACTTGAAATCTTACGAATCTTTCTTTCCC
Found at i:2851750 original size:17 final size:17
Alignment explanation
Indices: 2851703--2851739 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2851693 CATTGCGAAC
*
2851703 CTAAGACCTTTGTAAAT
1 CTAAAACCTTTGTAAAT
2851720 CTAAAAACCTTTGTAAAT
1 CT-AAAACCTTTGTAAAT
2851738 CT
1 CT
2851740 TAACTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (17 bp):
CTAAAACCTTTGTAAAT
Found at i:2852729 original size:3 final size:3
Alignment explanation
Indices: 2852721--2852811 Score: 79
Period size: 3 Copynumber: 32.3 Consensus size: 3
2852711 AGTATATCAC
*
2852721 TAT TAT TA- TAT TAT TAT TAT TA- TAC TA- TAT TA- TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
2852764 TAT TA- TAGT TAT TAT AAT AAT AAT TAT TAT TGT TAT TAT TAT T-T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2852808 TAT T
1 TAT T
2852812 TTTTTCTTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
2 14 0.18
3 60 0.79
4 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2852732 original size:5 final size:5
Alignment explanation
Indices: 2852700--2852779 Score: 56
Period size: 5 Copynumber: 15.4 Consensus size: 5
2852690 TTATTACTAG
* * * *
2852700 TATTA TAGTA TAGTA TATCA CTATTA T-TATA TTATTA TTATTA TACTA
1 TATTA TATTA TATTA TATTA -TATTA TAT-TA -TATTA -TATTA TATTA
*
2852748 TATTA TATTA TATTA TTATTA TAGT- TATTA TA
1 TATTA TATTA TATTA -TATTA TATTA TATTA TA
2852780 ATAATAATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.07
5 38 0.62
6 18 0.30
7 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (5 bp):
TATTA
Found at i:2853236 original size:21 final size:19
Alignment explanation
Indices: 2853178--2853240 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 19
2853168 TGGGGAATCC
*
2853178 TAGGTTTAATTTGAAGTTTT
1 TAGGTTTGATTT-AAGTTTT
* **
2853198 TAGGTTAGATTTGGGTTTT
1 TAGGTTTGATTTAAGTTTT
2853217 CTGAGGTTTGATTTAAGTTTT
1 -T-AGGTTTGATTTAAGTTTT
2853238 TAG
1 TAG
2853241 AAAATTTTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 7 0.21
20 12 0.35
21 15 0.44
ACGTcount: A:0.21, C:0.02, G:0.25, T:0.52
Consensus pattern (19 bp):
TAGGTTTGATTTAAGTTTT
Found at i:2853331 original size:19 final size:19
Alignment explanation
Indices: 2853307--2853356 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2853297 ATCTGGGTTT
2853307 GGATGAATTTTTCAATGGA
1 GGATGAATTTTTCAATGGA
*
2853326 GGATGAATTTTTCATTGGA
1 GGATGAATTTTTCAATGGA
*
2853345 GAATGAATTTTT
1 GGATGAATTTTT
2853357 TGATTGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (19 bp):
GGATGAATTTTTCAATGGA
Found at i:2853366 original size:13 final size:13
Alignment explanation
Indices: 2853348--2853372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2853338 CATTGGAGAA
2853348 TGAATTTTTTGAT
1 TGAATTTTTTGAT
2853361 TGAATTTTTTGA
1 TGAATTTTTTGA
2853373 CGAGGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (13 bp):
TGAATTTTTTGAT
Found at i:2857068 original size:33 final size:29
Alignment explanation
Indices: 2857030--2857107 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 29
2857020 AAGAGAAATG
2857030 AAAAAAAATAAAAAAAATGTGTGTAAAAAACA
1 AAAAAAAATAAAAAAAAT-T-TGT-AAAAACA
2857062 ACAAAAAAA-ACAAAAAAATTTGTAAAAACA
1 A-AAAAAAATA-AAAAAAATTTGTAAAAACA
*
2857092 AAAAAGAAGTAAAAAA
1 AAAAA-AAATAAAAAA
2857108 GAAAAAAGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
29 4 0.10
30 15 0.37
31 4 0.10
32 3 0.07
33 15 0.37
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (29 bp):
AAAAAAAATAAAAAAAATTTGTAAAAACA
Found at i:2857124 original size:9 final size:9
Alignment explanation
Indices: 2857091--2857138 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
2857081 TTGTAAAAAC
2857091 AAAAAAGAAG
1 AAAAAAG-AG
*
2857101 TAAAAA-AG
1 AAAAAAGAG
2857109 AAAAAAGAG
1 AAAAAAGAG
2857118 AAAAAAGAG
1 AAAAAAGAG
*
2857127 GAAAAAG-G
1 AAAAAAGAG
2857135 AAAA
1 AAAA
2857139 CTTAGACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 11 0.33
9 17 0.52
10 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:2858551 original size:86 final size:85
Alignment explanation
Indices: 2858432--2858768 Score: 390
Period size: 86 Copynumber: 3.9 Consensus size: 85
2858422 TCTGAAAGTC
*
2858432 CTTGCAT-TTTGTGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATG
1 CTTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATG
2858496 AATCTGAAAGTCCTTGTGAA
66 AATCTGAAAGTCCTTGTGAA
* * * * * *
2858516 CTTTGCATCTTTACGAATCTAGAACCTTTGTGAAACTT-AGAATTTTGTGAATATTTCTTTCTTG
1 C-TTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGA-AATCTTATGAATCTTTCTTTCTTA
** * *
2858580 CAAATCTAAAAGTCTTTGTGAA
64 TGAATCTGAAAGTCCTTGTGAA
* * * * * *
2858602 CCTTGCATCTTTGCAAATCTAGAACCTTTGTGAAACTTGAAATCTTGTAAATCTTTTTTTTTTAT
1 -CTTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTAT
* * **
2858667 GAATTTGAAAGTCTTTGCAAA
65 GAATCTGAAAGTCCTTGTGAA
* * * * *
2858688 CTTGAAATCTTTGCGAATCTAGAACCTTTGCGAAGCTTGAAATCTTACGAATCTTTCTTTCCTGT
1 CTTG-CATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTAT
2858753 GAATCTGAAAGTCCTT
65 GAATCTGAAAGTCCTT
2858769 ACGAACCTGA
Statistics
Matches: 209, Mismatches: 38, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
84 1 0.00
85 11 0.05
86 195 0.93
87 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (85 bp):
CTTGCATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATG
AATCTGAAAGTCCTTGTGAA
Found at i:2858654 original size:34 final size:34
Alignment explanation
Indices: 2858575--2858655 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
2858565 AATATTTCTT
* * *
2858575 TCTTGCAAATCTAAAAGTCTTTGTGAACCTTGCA
1 TCTTGCAAATCTAAAAGCCTTTGTGAAACTTGAA
*
2858609 TCTTTGCAAATCTAGAA-CCTTTGTGAAACTTGAAA
1 TC-TTGCAAATCTAAAAGCCTTTGTGAAACTTG-AA
*
2858644 TCTTGTAAATCT
1 TCTTGCAAATCT
2858656 TTTTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 24 0.60
35 16 0.40
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (34 bp):
TCTTGCAAATCTAAAAGCCTTTGTGAAACTTGAA
Found at i:2858700 original size:17 final size:18
Alignment explanation
Indices: 2858671--2858733 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
2858661 TTTTATGAAT
2858671 TTGAAAGTCTTTGC-AAAC
1 TTGAAA-TCTTTGCGAAAC
*
2858689 TTGAAATCTTTGCGAATC
1 TTGAAATCTTTGCGAAAC
* * *
2858707 TAG-AACCTTTGCGAAGC
1 TTGAAATCTTTGCGAAAC
2858724 TTGAAATCTT
1 TTGAAATCTT
2858734 ACGAATCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 21 0.57
18 16 0.43
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (18 bp):
TTGAAATCTTTGCGAAAC
Found at i:2858780 original size:86 final size:85
Alignment explanation
Indices: 2858439--2858817 Score: 366
Period size: 86 Copynumber: 4.4 Consensus size: 85
2858429 GTCCTTGCAT
*
2858439 TTTGTGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
* * *
2858504 AGTCCTTGTGAACTTTGCATC
66 AGTCCTTGCGAAC-CTGAATC
* * * * * *** *
2858525 TTTACGAATCTAGAACCTTTGTGAAACTT-AGAATTTTGTGAATATTTCTTTCTTGCAAATCTAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGA-AATCTTATGAATCTTTCTTTCTTATGAATCTGA
* * *
2858589 AAGTCTTTGTGAACCTTGCATC
65 AAGTCCTTGCGAACC-TGAATC
* * * * * * *
2858611 TTTGCAAATCTAGAACCTTTGTGAAACTTGAAATCTTGTAAATCTTTTTTTTTTATGAATTTGAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
* * *
2858676 AGTCTTTGCAAACTTGAAATC
66 AGTCCTTGCGAACCTG-AATC
* * * *
2858697 TTTGCGAATCTAGAACCTTTGCGAAGCTTGAAATCTTACGAATCTTTCTTTCCTGTGAATCTGAA
1 TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
* *
2858762 AGTCCTTACGAACCTGAAACC
66 AGTCCTTGCGAACCTG-AATC
* * * *
2858783 TTTACGAATTTGAAAACCTTTGCGAATCTT-AAATC
1 TTTGCGAATCT-AGAACCTTTGCGAAACTTGAAATC
2858818 CTTGTTAAAA
Statistics
Matches: 240, Mismatches: 48, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
85 3 0.01
86 220 0.92
87 17 0.07
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (85 bp):
TTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTATGAATCTTTCTTTCTTATGAATCTGAA
AGTCCTTGCGAACCTGAATC
Found at i:2862901 original size:11 final size:11
Alignment explanation
Indices: 2862885--2862924 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2862875 CAATCTTTTG
2862885 TCTATTAGTTT
1 TCTATTAGTTT
*
2862896 TCTATTGGTTT
1 TCTATTAGTTT
2862907 TCTATTAAGTTT
1 TCTATT-AGTTT
2862919 T-TATTA
1 TCTATTA
2862925 TTCTCAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 1 0.04
11 20 0.77
12 5 0.19
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.62
Consensus pattern (11 bp):
TCTATTAGTTT
Found at i:2863164 original size:19 final size:20
Alignment explanation
Indices: 2863142--2863181 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2863132 ATGTAATTCA
*
2863142 ATTTTAAGTTTAAGTT-ATT
1 ATTTTAAGATTAAGTTGATT
*
2863161 ATTTTGAGATTAAGTTGATT
1 ATTTTAAGATTAAGTTGATT
2863181 A
1 A
2863182 GACTGCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (20 bp):
ATTTTAAGATTAAGTTGATT
Found at i:2866237 original size:21 final size:23
Alignment explanation
Indices: 2866193--2866239 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
2866183 TTAAAAAAAA
*
2866193 AAAAAACTTTTTTAATGTAATAG
1 AAAAAACTTATTTAATGTAATAG
*
2866216 AAAAAAC-TATTTAAT-TATTAG
1 AAAAAACTTATTTAATGTAATAG
2866237 AAA
1 AAA
2866240 CGTGTTGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.36
Consensus pattern (23 bp):
AAAAAACTTATTTAATGTAATAG
Found at i:2867082 original size:14 final size:14
Alignment explanation
Indices: 2867056--2867111 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
2867046 AATATAGCAT
2867056 AATTTTT-AGAAATA
1 AATTTTTGA-AAATA
2867070 AATTTTTGAAAATCTA
1 AATTTTTGAAAA--TA
* *
2867086 TATTCTTGAAAATA
1 AATTTTTGAAAATA
2867100 AATTTTTGAAAA
1 AATTTTTGAAAA
2867112 CTTAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 22 0.63
15 1 0.03
16 12 0.34
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTTTTGAAAATA
Found at i:2867536 original size:25 final size:23
Alignment explanation
Indices: 2867508--2867577 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 23
2867498 GGAATTTTCT
2867508 TGAAAATATTTATAAATTAATATAA
1 TGAAAA-ATTTATAAATTAATA-AA
2867533 TGAAAAATGTTAT-AATTAA-AAA
1 TGAAAAAT-TTATAAATTAATAAA
*
2867555 TAATAAAATTTA-AAATTAATAAA
1 TGA-AAAATTTATAAATTAATAAA
2867578 AAATTTACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 13 0.32
23 9 0.22
24 8 0.20
25 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
TGAAAAATTTATAAATTAATAAA
Found at i:2867567 original size:16 final size:16
Alignment explanation
Indices: 2867548--2867578 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2867538 AATGTTATAA
2867548 TTAAAAATAATAAAAT
1 TTAAAAATAATAAAAT
*
2867564 TTAAAATTAATAAAA
1 TTAAAAATAATAAAA
2867579 AATTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAAATAATAAAAT
Found at i:2869865 original size:24 final size:24
Alignment explanation
Indices: 2869837--2869885 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2869827 TATAAGCTAA
2869837 AAAAACTACTATCTTATATTGCAAT
1 AAAAA-TACTATCTTATATTGCAAT
* *
2869862 AAAAATATTATTTTATATTGCAAT
1 AAAAATACTATCTTATATTGCAAT
2869886 TGTCCAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (24 bp):
AAAAATACTATCTTATATTGCAAT
Found at i:2869906 original size:3 final size:3
Alignment explanation
Indices: 2869898--2869932 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2869888 TCCAAGATCA
2869898 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2869933 AACGTGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2870858 original size:14 final size:13
Alignment explanation
Indices: 2870820--2870859 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
2870810 CTCAAAGCTA
*
2870820 ATTTTTTTTTATT
1 ATTTTTTTTTCTT
2870833 ATTTTTCTTTTCTT
1 ATTTTT-TTTTCTT
2870847 ATTTATTTTTTCT
1 ATTT-TTTTTTCT
2870860 AACAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.25
14 16 0.67
15 2 0.08
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTCTT
Found at i:2880727 original size:26 final size:26
Alignment explanation
Indices: 2880684--2880736 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2880674 ATAATTGAAC
*
2880684 ATGTTTTTATCCATTTATTTAAATGG
1 ATGTTTTTATCCACTTATTTAAATGG
** *
2880710 ATGTTTTTATCTGCTTATTTAATTGG
1 ATGTTTTTATCCACTTATTTAAATGG
2880736 A
1 A
2880737 GATTAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.55
Consensus pattern (26 bp):
ATGTTTTTATCCACTTATTTAAATGG
Found at i:2881703 original size:10 final size:10
Alignment explanation
Indices: 2881687--2881841 Score: 126
Period size: 10 Copynumber: 16.1 Consensus size: 10
2881677 ATATTCCAAG
2881687 AAATTCTAAA
1 AAATTCTAAA
2881697 AAATTCT--A
1 AAATTCTAAA
**
2881705 AAATTAGAAA
1 AAATTCTAAA
2881715 AAATTCT-AA
1 AAATTCTAAA
* * *
2881724 AATTTTTTAA
1 AAATTCTAAA
* *
2881734 AAATTATAGA
1 AAATTCTAAA
2881744 AAATTCTAAA
1 AAATTCTAAA
2881754 AAATT-TAAA
1 AAATTCTAAA
*
2881763 AAGTTC-AAA
1 AAATTCTAAA
*
2881772 AAAATCTAAA
1 AAATTCTAAA
* *
2881782 ACATT-AAAA
1 AAATTCTAAA
* *
2881791 AAATTTTAAG
1 AAATTCTAAA
2881801 AAATTCTAAA
1 AAATTCTAAA
2881811 AAATTCTAAA
1 AAATTCTAAA
*
2881821 AATTTTCT-AA
1 AA-ATTCTAAA
2881831 AAATTCTAAA
1 AAATTCTAAA
2881841 A
1 A
2881842 TAAATTTCCA
Statistics
Matches: 112, Mismatches: 25, Indels: 16
0.73 0.16 0.10
Matches are distributed among these distances:
8 6 0.05
9 33 0.29
10 69 0.62
11 4 0.04
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (10 bp):
AAATTCTAAA
Found at i:2881752 original size:57 final size:57
Alignment explanation
Indices: 2881684--2881821 Score: 167
Period size: 57 Copynumber: 2.4 Consensus size: 57
2881674 AAGATATTCC
** **
2881684 AAGAAATTCTAAAAAATTCTAAAA-TT-AGAAAAAATTCTAAAATTTTTTAAAAATTAT
1 AAGAAATTCTAAAAAATTCTAAAAGTTCA-AAAAAA-TCTAAAACATTAAAAAAATTAT
*
2881741 -AGAAAATTCTAAAAAATT-TAAAAAGTTCAAAAAAATCTAAAACATTAAAAAAATTTT
1 AAG-AAATTCTAAAAAATTCT-AAAAGTTCAAAAAAATCTAAAACATTAAAAAAATTAT
2881798 AAGAAATTCTAAAAAATTCTAAAA
1 AAGAAATTCTAAAAAATTCTAAAA
2881822 ATTTTCTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
56 3 0.04
57 55 0.79
58 11 0.16
59 1 0.01
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (57 bp):
AAGAAATTCTAAAAAATTCTAAAAGTTCAAAAAAATCTAAAACATTAAAAAAATTAT
Found at i:2881822 original size:29 final size:29
Alignment explanation
Indices: 2881684--2881841 Score: 135
Period size: 29 Copynumber: 5.5 Consensus size: 29
2881674 AAGATATTCC
**
2881684 AAGAAATTCTAAAAAATTCT-AAAATTAG
1 AAGAAATTCTAAAAAATTCTAAAAATTTT
* ** * *
2881712 AAAAAATTCTAAAATTTTTTAAAAATTAT
1 AAGAAATTCTAAAAAATTCTAAAAATTTT
* *
2881741 -AGAAAATTCTAAAAAATT-TAAAAAGTTC
1 AAG-AAATTCTAAAAAATTCTAAAAATTTT
* * * **
2881769 AAAAAAATCTAAAACATTAAAAAAATTTT
1 AAGAAATTCTAAAAAATTCTAAAAATTTT
2881798 AAGAAATTCTAAAAAATTCTAAAAATTTTCT
1 AAGAAATTCTAAAAAATTCTAAAAA-TTT-T
2881829 AA-AAATTCTAAAA
1 AAGAAATTCTAAAA
2881842 TAAATTTCCA
Statistics
Matches: 102, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
28 37 0.36
29 48 0.47
30 14 0.14
31 3 0.03
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (29 bp):
AAGAAATTCTAAAAAATTCTAAAAATTTT
Found at i:2882067 original size:9 final size:8
Alignment explanation
Indices: 2882018--2882135 Score: 58
Period size: 8 Copynumber: 13.0 Consensus size: 8
2882008 CCTGAAACTT
2882018 TTTAAAATA
1 TTTAAAA-A
2882027 TTTAAATAA
1 TTTAAA-AA
*
2882036 TTT-AACA
1 TTTAAAAA
2882043 TTTAAAAA
1 TTTAAAAA
*
2882051 TTTTAAAA
1 TTTAAAAA
2882059 TTTCAAAAAAAA
1 TTT----AAAAA
2882071 TTCTAAAAA
1 TT-TAAAAA
2882080 CTATTAAAAA
1 -T-TTAAAAA
2882090 TTTTTAAAAA
1 --TTTAAAAA
*
2882100 TTAAAAAA
1 TTTAAAAA
2882108 TTCTAGAAAA
1 TT-TA-AAAA
2882118 TTTTAGAAAA
1 -TTTA-AAAA
*
2882128 TTCAAAAA
1 TTTAAAAA
2882136 GAATTAAGGC
Statistics
Matches: 88, Mismatches: 8, Indels: 27
0.72 0.07 0.22
Matches are distributed among these distances:
7 4 0.05
8 28 0.32
9 19 0.22
10 26 0.30
11 4 0.05
12 6 0.07
13 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (8 bp):
TTTAAAAA
Found at i:2882287 original size:20 final size:20
Alignment explanation
Indices: 2882264--2882309 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2882254 AAATTAAAAT
2882264 AAAAATAAAAATAA-TTTTTA
1 AAAAAT-AAAATAACTTTTTA
*
2882284 AAAAATATAATAACTTTTTA
1 AAAAATAAAATAACTTTTTA
2882304 AAAAAT
1 AAAAAT
2882310 TTTAAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATAAAATAACTTTTTA
Found at i:2882424 original size:20 final size:19
Alignment explanation
Indices: 2882397--2882472 Score: 98
Period size: 20 Copynumber: 3.9 Consensus size: 19
2882387 ATTTTTGAAA
2882397 AAATTTTAAAATTTTTTAG
1 AAATTTTAAAATTTTTTAG
* * *
2882416 AATTGTTTAAAACTTTTAAG
1 AAAT-TTTAAAATTTTTTAG
2882436 AAATTTTAAAATTTTTTAAG
1 AAATTTTAAAATTTTTT-AG
*
2882456 AAATTCTAAAATTTTTT
1 AAATTTTAAAATTTTTT
2882473 TGCATACTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
19 14 0.29
20 34 0.71
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
AAATTTTAAAATTTTTTAG
Found at i:2882440 original size:39 final size:39
Alignment explanation
Indices: 2882371--2882454 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
2882361 TTTTTATAAA
* *
2882371 TTTTAAAATGTTTATAATTTTTGAAAAAATTTTAAAATT
1 TTTTAAAATGTTTAAAACTTTTGAAAAAATTTTAAAATT
* *
2882410 TTTTAGAATTGTTTAAAACTTTT-AAGAAATTTTAAAATT
1 TTTTA-AAATGTTTAAAACTTTTGAAAAAATTTTAAAATT
2882449 TTTTAA
1 TTTTAA
2882455 GAAATTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.03
39 25 0.62
40 14 0.35
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (39 bp):
TTTTAAAATGTTTAAAACTTTTGAAAAAATTTTAAAATT
Found at i:2882572 original size:10 final size:9
Alignment explanation
Indices: 2882544--2882644 Score: 53
Period size: 10 Copynumber: 10.6 Consensus size: 9
2882534 TTTTGAAATG
2882544 AAAATTTTTT
1 AAAA-TTTTT
2882554 ATAAA-TTTT
1 A-AAATTTTT
2882563 AAATATTTTT
1 AAA-ATTTTT
*
2882573 CAAAGTTTTT
1 -AAAATTTTT
2882583 AAAAATTTTTT
1 -AAAA-TTTTT
*
2882594 AGAATTATTT
1 AAAATT-TTT
**
2882604 TGAATTTTT
1 AAAATTTTT
*
2882613 ATAAGTTTTT
1 A-AAATTTTT
2882623 AAAA-TTTT
1 AAAATTTTT
* *
2882631 AGAATTTTA
1 AAAATTTTT
2882640 AAAAT
1 AAAAT
2882645 ATATTTTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
8 9 0.13
9 20 0.28
10 31 0.44
11 11 0.15
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (9 bp):
AAAATTTTT
Found at i:2882572 original size:20 final size:20
Alignment explanation
Indices: 2882544--2882594 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2882534 TTTTGAAATG
2882544 AAAATTTTTTATAA-ATTTTA
1 AAAATTTTTTA-AAGATTTTA
* * *
2882564 AATATTTTTCAAAGTTTTTA
1 AAAATTTTTTAAAGATTTTA
2882584 AAAATTTTTTA
1 AAAATTTTTTA
2882595 GAATTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
AAAATTTTTTAAAGATTTTA
Found at i:2882613 original size:19 final size:18
Alignment explanation
Indices: 2882589--2882638 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2882579 TTTTAAAAAT
*
2882589 TTTTTAGAATTATTTTGAA
1 TTTTTAGAATT-TTTTAAA
* *
2882608 TTTTTATAAGTTTTTAAA
1 TTTTTAGAATTTTTTAAA
*
2882626 ATTTTAGAATTTT
1 TTTTTAGAATTTT
2882639 AAAAATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
TTTTTAGAATTTTTTAAA
Found at i:2882712 original size:22 final size:22
Alignment explanation
Indices: 2882658--2882714 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2882648 TTTTAAAAAA
* *
2882658 TTAGA-TTTTTTTTCAAGTTTT
1 TTAGAGTTTTTTTTAAAATTTT
* **
2882679 TTTGAGAATTTTTTAAAATTTT
1 TTAGAGTTTTTTTTAAAATTTT
2882701 TTAGAGTTTTTTTT
1 TTAGAGTTTTTTTT
2882715 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.65
Consensus pattern (22 bp):
TTAGAGTTTTTTTTAAAATTTT
Found at i:2882745 original size:11 final size:12
Alignment explanation
Indices: 2882721--2882754 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2882711 TTTTTTGTAA
2882721 TTTTTAAAATTT
1 TTTTTAAAATTT
*
2882733 TTTTTGAAATTT
1 TTTTTAAAATTT
2882745 TCTTTTAAAA
1 T-TTTTAAAA
2882755 ATGATGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTTTAAAATTT
Found at i:2887504 original size:194 final size:198
Alignment explanation
Indices: 2887225--2887631 Score: 556
Period size: 194 Copynumber: 2.1 Consensus size: 198
2887215 TTAGAGAAAG
** * * *
2887225 ATCAATTAAGGTGTTCAAAGCACAAAATGCCTTAATAGATCCTTTTTAAAAATTTGTAATTTATG
1 ATCAATTAAGGCATTCAAAGCACAAAATGCCTTAATAGATCATTTTTAAAAATTTATAATTGATG
2887290 GTTTTGAAAATGAACAATTTGTTATGATATTTGTCTATTAAATTAATCAAAAAA-TTA-TTTTTA
66 GTTTTGAAAATGAACAATTTGTTATGATATTTGTCTATTAAATTAATCAAAAAATTTATTTTTTA
* * * * * ***
2887353 TAAATCAATTAAGGTGTTTTTGTACATAAACACCTTAATTGATGATGT-TTTC-TAATTATAAAA
131 TAAATCAATTAAGGCGTTTCTATACACAAACACCTTAATTGATGATATCCCACATAATTATAAAA
2887416 C-A
196 CTA
* * * *
2887418 TATCAATTAAGGCATTCAAAGTACATAAATGCCTTAATTGTTCATTTTTAATAA-TTATAATTGA
1 -ATCAATTAAGGCATTCAAAGCACA-AAATGCCTTAATAGATCATTTTTAAAAATTTATAATTGA
*
2887482 TGGTTTTGAAAATGATCAATTTGTTATGATATTTGTCTATTAAATTAATCAAAAAATTTATTTTT
64 TGGTTTTGAAAATGAACAATTTGTTATGATATTTGTCTATTAAATTAATCAAAAAATTTATTTTT
* * **
2887547 TTTAGATCAATTAAGGCGTTTCTATACACAAATGCCTTAATTGATGATATCCCACATAATTATAA
129 TATAAATCAATTAAGGCGTTTCTATACACAAACACCTTAATTGATGATATCCCACATAATTATAA
2887612 AACTA
194 AACTA
2887617 ATCAATTAAGGCATT
1 ATCAATTAAGGCATT
2887632 TGTGTCCAAA
Statistics
Matches: 185, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
194 84 0.45
195 27 0.15
196 45 0.24
197 1 0.01
198 27 0.15
199 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (198 bp):
ATCAATTAAGGCATTCAAAGCACAAAATGCCTTAATAGATCATTTTTAAAAATTTATAATTGATG
GTTTTGAAAATGAACAATTTGTTATGATATTTGTCTATTAAATTAATCAAAAAATTTATTTTTTA
TAAATCAATTAAGGCGTTTCTATACACAAACACCTTAATTGATGATATCCCACATAATTATAAAA
CTA
Found at i:2890138 original size:17 final size:18
Alignment explanation
Indices: 2890116--2890151 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2890106 TTTTGTGTAA
2890116 TTACTATTATTTTT-TGT
1 TTACTATTATTTTTATGT
*
2890133 TTACTATTGTTTTTATGT
1 TTACTATTATTTTTATGT
2890151 T
1 T
2890152 CAATTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (18 bp):
TTACTATTATTTTTATGT
Found at i:2890678 original size:22 final size:22
Alignment explanation
Indices: 2890648--2890692 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2890638 TATGATTAGA
2890648 TATTATTTAATT-TTTATTAGTT
1 TATTATTT-ATTGTTTATTAGTT
* *
2890670 TATTGTTTATTGTTTATTGGTT
1 TATTATTTATTGTTTATTAGTT
2890692 T
1 T
2890693 TGTTTTTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (22 bp):
TATTATTTATTGTTTATTAGTT
Found at i:2890692 original size:15 final size:15
Alignment explanation
Indices: 2890648--2890688 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2890638 TATGATTAGA
2890648 TATTA-TTTAATT-TT
1 TATTAGTTT-ATTGTT
2890662 TATTAGTTTATTGTT
1 TATTAGTTTATTGTT
2890677 TATT-GTTTATTG
1 TATTAGTTTATTG
2890689 GTTTTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (15 bp):
TATTAGTTTATTGTT
Found at i:2890701 original size:6 final size:7
Alignment explanation
Indices: 2890660--2890706 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
2890650 TTATTTAATT
2890660 TTTATTAG
1 TTTATT-G
2890668 TTTATTG
1 TTTATTG
2890675 TTTATTG
1 TTTATTG
2890682 TTTATTG
1 TTTATTG
*
2890689 GTT-TTG
1 TTTATTG
2890695 TTT-TTG
1 TTTATTG
2890701 TCTTAT
1 T-TTAT
2890707 ATCATGGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 9 0.26
7 19 0.54
8 7 0.20
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (7 bp):
TTTATTG
Found at i:2895180 original size:143 final size:144
Alignment explanation
Indices: 2894918--2895222 Score: 341
Period size: 143 Copynumber: 2.1 Consensus size: 144
2894908 ACTCTTAGGA
**
2894918 GTATTTTTGTAATTTGACAATTTTGACGTAATTTTTTCACAAAACACTCTAGATCATGGTTTTCT
1 GTATTTTTGTAATTTGACAATTTTGACGTAATTTTTTCACAAAACACTCTAGATCATGGTTTTAA
* * * * * *
2894983 ATTATTTCATGATTTTTAGTGTAGTAAAAACTTTGATTGCACCTCGAAATGTGTGAAATTACTAA
66 ATTATTTCATGATTTTTAGTGCAGTAAAAACCTTGATCGCACCTAGAAAGGTGTGAAATTACAAA
** *
2895048 AATACTTTTTAAGG
131 AATACACTTTAAAG
* * * * *
2895062 GTATTTTTGTAATTT-A-ACTTTCTAGAGGTCATTTTTT-GCAAAACATTCTAGATCAT-GTTTT
1 GTATTTTTGTAATTTGACAATTT-T-GACGTAATTTTTTCACAAAACACTCTAGATCATGGTTTT
* * * *
2895123 AAAATTATTTTATGATTTTTGGTGCATTGAAAACCTTGATCGCACCTTAG-AAGGTGTGAAATTA
64 -AAATTATTTCATGATTTTTAGTGCAGTAAAAACCTTGATCGCACC-TAGAAAGGTGTGAAATTA
2895187 CAAAAATACACTTTAAAG
127 CAAAAATACACTTTAAAG
**
2895205 GTATTTTCATAATTTGAC
1 GTATTTTTGTAATTTGAC
2895223 CTTCTCGAGA
Statistics
Matches: 133, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
142 9 0.07
143 95 0.71
144 29 0.22
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (144 bp):
GTATTTTTGTAATTTGACAATTTTGACGTAATTTTTTCACAAAACACTCTAGATCATGGTTTTAA
ATTATTTCATGATTTTTAGTGCAGTAAAAACCTTGATCGCACCTAGAAAGGTGTGAAATTACAAA
AATACACTTTAAAG
Found at i:2898965 original size:37 final size:37
Alignment explanation
Indices: 2898915--2898988 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2898905 TAATAACAAC
2898915 TTAACAATACAGTAAATTAAAATATGCAGTAGCCAAA
1 TTAACAATACAGTAAATTAAAATATGCAGTAGCCAAA
2898952 TTAACAATACAGTAAATTAAAATATGCAGTAGCCAAA
1 TTAACAATACAGTAAATTAAAATATGCAGTAGCCAAA
2898989 AAGTAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (37 bp):
TTAACAATACAGTAAATTAAAATATGCAGTAGCCAAA
Found at i:2898970 original size:16 final size:15
Alignment explanation
Indices: 2898915--2898975 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 15
2898905 TAATAACAAC
2898915 TTAACAATACAGTAAA
1 TTAA-AATACAGTAAA
2898931 TTAAAATATGCAGTAGCCAAA
1 TTAAAATA--CAGT----AAA
2898952 TTAACAATACAGTAAA
1 TTAA-AATACAGTAAA
2898968 TTAAAATA
1 TTAAAATA
2898976 TGCAGTAGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
15 8 0.21
16 11 0.29
17 4 0.11
20 4 0.11
21 7 0.18
22 4 0.11
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.26
Consensus pattern (15 bp):
TTAAAATACAGTAAA
Found at i:2900440 original size:9 final size:9
Alignment explanation
Indices: 2900426--2900486 Score: 70
Period size: 9 Copynumber: 6.6 Consensus size: 9
2900416 AAACAACATA
2900426 AAAAAATAT
1 AAAAAATAT
*
2900435 AAAAAAAATT
1 AAAAAATA-T
2900445 AAAAAATAT
1 AAAAAATAT
*
2900454 AAGAAATAT
1 AAAAAATAT
2900463 AAAAAATAT
1 AAAAAATAT
2900472 ATAAATAATA-
1 A-AAA-AATAT
2900482 AAAAA
1 AAAAA
2900487 GAAAACTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
8 1 0.02
9 28 0.62
10 12 0.27
11 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAAAATAT
Found at i:2900441 original size:11 final size:11
Alignment explanation
Indices: 2900425--2900476 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
2900415 CAAACAACAT
2900425 AAAAAAATATA
1 AAAAAAATATA
2900436 AAAAAAAT-T-
1 AAAAAAATATA
2900445 -AAAAAATAT-
1 AAAAAAATATA
*
2900454 -AAGAAATATA
1 AAAAAAATATA
*
2900464 AAAAATATATA
1 AAAAAAATATA
2900475 AA
1 AA
2900477 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 7 0.20
9 9 0.26
10 1 0.03
11 18 0.51
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAAAAATATA
Found at i:2900465 original size:18 final size:18
Alignment explanation
Indices: 2900426--2900486 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
2900416 AAACAACATA
*
2900426 AAAAAATATAAAAAAAATT
1 AAAAAATATAAAAAATA-T
*
2900445 AAAAAATATAAGAAATAT
1 AAAAAATATAAAAAATAT
2900463 AAAAAATATATAAATAATA-
1 AAAAAATATA-AAA-AATAT
2900482 AAAAA
1 AAAAA
2900487 GAAAACTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 11 0.30
19 22 0.59
20 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAAATATAAAAAATAT
Found at i:2901924 original size:2 final size:2
Alignment explanation
Indices: 2901917--2901946 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2901907 TCTAAGGTTT
2901917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2901947 AAGAGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2902113 original size:21 final size:21
Alignment explanation
Indices: 2902087--2902142 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2902077 TGAGGAATTA
*
2902087 AATAAAATAATAAAAAGAAAT
1 AATAAAATAATAAAAACAAAT
**
2902108 AATAAACATAA-AAATTCAAAT
1 AATAAA-ATAATAAAAACAAAT
2902129 AATACAAATAATAA
1 AATA-AAATAATAA
2902143 TAGAAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (21 bp):
AATAAAATAATAAAAACAAAT
Found at i:2902775 original size:26 final size:27
Alignment explanation
Indices: 2902709--2902776 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
2902699 AATTTTTAAA
*
2902709 CCTTAAAATGAAAACCTAATGTGAAAC
1 CCTTAAAATGAAACCCTAATGTGAAAC
** *
2902736 CCTTAAAACAAAACCCTAGTGTGAAAC
1 CCTTAAAATGAAACCCTAATGTGAAAC
*
2902763 TC-TAAAATGAAACC
1 CCTTAAAATGAAACC
2902777 TTAAAACAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 10 0.29
27 24 0.71
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (27 bp):
CCTTAAAATGAAACCCTAATGTGAAAC
Found at i:2902960 original size:19 final size:19
Alignment explanation
Indices: 2902932--2902970 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2902922 AAAATAAAAT
2902932 CCTAGATGAAACCCTAAAC
1 CCTAGATGAAACCCTAAAC
* *
2902951 CCTAGGTGAAATCCTAAAC
1 CCTAGATGAAACCCTAAAC
2902970 C
1 C
2902971 TTAAGTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (19 bp):
CCTAGATGAAACCCTAAAC
Found at i:2902978 original size:19 final size:19
Alignment explanation
Indices: 2902938--2902979 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2902928 AAATCCTAGA
*
2902938 TGAAACCCTAAACCCTAGG
1 TGAAACCCTAAACCCTAAG
* *
2902957 TGAAATCCTAAACCTTAAG
1 TGAAACCCTAAACCCTAAG
2902976 TGAA
1 TGAA
2902980 GTCCAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (19 bp):
TGAAACCCTAAACCCTAAG
Found at i:2906955 original size:3 final size:3
Alignment explanation
Indices: 2906947--2906986 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2906937 ATAAGGAAAT
2906947 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2906987 GATGATGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2906991 original size:3 final size:3
Alignment explanation
Indices: 2906985--2907013 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2906975 AATAATAATA
2906985 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2907014 ATTATACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2908926 original size:16 final size:15
Alignment explanation
Indices: 2908905--2908975 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
2908895 GAAAAAAAGG
2908905 AAAGAAAGAACAAAA
1 AAAGAAAGAACAAAA
* *
2908920 TAAAGAAAGAATAACA
1 -AAAGAAAGAACAAAA
2908936 AAAGAAAAGAAGCAAAA
1 AAAG-AAAGAA-CAAAA
* * *
2908953 GAAAGAAAAAAGAAGA
1 -AAAGAAAGAACAAAA
2908969 AAAGAAA
1 AAAGAAA
2908976 TAAATGGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.24
16 22 0.49
17 8 0.18
18 4 0.09
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAACAAAA
Found at i:2908944 original size:20 final size:20
Alignment explanation
Indices: 2908896--2908946 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2908886 TAAAAAAGAG
*
2908896 AAAAAAAGGAAAGAAAGAAC
1 AAAAAAAAGAAAGAAAGAAC
* *
2908916 AAAATAAAGAAAG-AATAAC
1 AAAAAAAAGAAAGAAAGAAC
2908935 AAAAGAAAAGAA
1 AAAA-AAAAGAA
2908947 GCAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAAGAAC
Found at i:2908953 original size:14 final size:14
Alignment explanation
Indices: 2908932--2908975 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2908922 AAGAAAGAAT
2908932 AACAAAAGAAAAGA
1 AACAAAAGAAAAGA
*
2908946 AGCAAAAG-AAAGA
1 AACAAAAGAAAAGA
*
2908959 AAAAAGAAGAAAAGA
1 AACAA-AAGAAAAGA
2908974 AA
1 AA
2908976 TAAATGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 8 0.32
14 10 0.40
15 7 0.28
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (14 bp):
AACAAAAGAAAAGA
Found at i:2910078 original size:22 final size:22
Alignment explanation
Indices: 2910009--2910146 Score: 73
Period size: 22 Copynumber: 6.3 Consensus size: 22
2909999 TAAGCCCAAT
* * * *
2910009 TTAGCTGGCATGTAAACTTAGA
1 TTAGTTGGCACGTAAGCCTAGA
* * **
2910031 TTTGTTGGCACATAAG-CTCATT
1 TTAGTTGGCACGTAAGCCT-AGA
2910053 TTAGTTGGCACGTAAGCCTAGA
1 TTAGTTGGCACGTAAGCCTAGA
* ** * * *
2910075 TTAGTTAGCTTGCAAGCCCATA
1 TTAGTTGGCACGTAAGCCTAGA
* * ** *
2910097 TTAGCTAGCATATAA-CCTCAGT
1 TTAGTTGGCACGTAAGCCT-AGA
2910119 TTAGTTGGCACGTAAGCCTAGA
1 TTAGTTGGCACGTAAGCCTAGA
2910141 TTAGTT
1 TTAGTT
2910147 AAAAAATTAT
Statistics
Matches: 82, Mismatches: 30, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
21 3 0.04
22 74 0.90
23 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (22 bp):
TTAGTTGGCACGTAAGCCTAGA
Found at i:2910381 original size:32 final size:32
Alignment explanation
Indices: 2910294--2910543 Score: 211
Period size: 32 Copynumber: 7.8 Consensus size: 32
2910284 CTTGAGCAAG
* * *
2910294 AATTTAGGCCTAGTTTGGCTGGCACCAATGGA
1 AATTTAAGCCTAGTTTAGCTGGCACCAATGAA
* * * *
2910326 AATGTAAGCTTAATTTAGTTGGCACCAATGAA
1 AATTTAAGCCTAGTTTAGCTGGCACCAATGAA
* * *
2910358 AATTTAAGCCCAGTCTAGCTGGCACTTAAT-AA
1 AATTTAAGCCTAGTTTAGCTGGCAC-CAATGAA
* * *
2910390 GAATTTAAGCCTAGTGTAGCTGGCATCAATTAA
1 -AATTTAAGCCTAGTTTAGCTGGCACCAATGAA
*
2910423 AATTTAAGCCTAGTTTAGCTGACACCCAATGAA
1 AATTTAAGCCTAGTTTAGCTGGCA-CCAATGAA
** * * *
2910456 GTTTTAA-ACTCAGTTTAG-TCGGTACTTAATGAA
1 AATTTAAGCCT-AGTTTAGCT-GGCAC-CAATGAA
** *
2910489 AATTTAAGCC-AAATTATCTGGCACCAATGAA
1 AATTTAAGCCTAGTTTAGCTGGCACCAATGAA
*
2910520 AATTTAAGCCTAGTTTAGTTGGCA
1 AATTTAAGCCTAGTTTAGCTGGCA
2910544 TCGAAAAGTC
Statistics
Matches: 168, Mismatches: 40, Indels: 20
0.74 0.18 0.09
Matches are distributed among these distances:
31 16 0.10
32 92 0.55
33 59 0.35
34 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (32 bp):
AATTTAAGCCTAGTTTAGCTGGCACCAATGAA
Found at i:2910536 original size:97 final size:97
Alignment explanation
Indices: 2910311--2910537 Score: 253
Period size: 97 Copynumber: 2.3 Consensus size: 97
2910301 GCCTAGTTTG
* * * * * * *
2910311 GCTGGCACCAATGGAAATGTAAGCTTAATTTAGTTGGCACCAATGAAAATTTAAGCCCAGTCTAG
1 GCTGGCACCAATGAAAATTTAAGCCTAGTTTAGCTGACACCAATGAAAATTTAAACCCAGTCTAG
* *
2910376 CTGGCACTTAATAAGAATTTAAGCCTAGTGTA
66 CTGGCACTTAATAAGAATTTAAGCCAAATGTA
* * ** * *
2910408 GCTGGCATCAATTAAAATTTAAGCCTAGTTTAGCTGACACCCAATGAAGTTTTAAACTCAGTTTA
1 GCTGGCACCAATGAAAATTTAAGCCTAGTTTAGCTGACA-CCAATGAAAATTTAAACCCAGTCTA
*
2910473 G-TCGGTACTTAATGAA-AATTTAAGCCAAAT-TA
65 GCT-GGCACTTAAT-AAGAATTTAAGCCAAATGTA
*
2910505 TCTGGCACCAATGAAAATTTAAGCCTAGTTTAG
1 GCTGGCACCAATGAAAATTTAAGCCTAGTTTAG
2910538 TTGGCATCGA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
97 64 0.59
98 42 0.39
99 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (97 bp):
GCTGGCACCAATGAAAATTTAAGCCTAGTTTAGCTGACACCAATGAAAATTTAAACCCAGTCTAG
CTGGCACTTAATAAGAATTTAAGCCAAATGTA
Found at i:2910593 original size:28 final size:28
Alignment explanation
Indices: 2910518--2910596 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 28
2910508 GGCACCAATG
* *
2910518 AAAATTTAAGCCTAGTTTAGTTGGCATCG
1 AAAATTTAAGCC-AGTTTAGTTGGCAACC
2910547 AAAAGTCTTAAGCCCAGTTTAGTTGG-AACC
1 AAAA-T-TTAAG-CCAGTTTAGTTGGCAACC
*
2910577 TAAATTTAAGCTCAGTTTAG
1 AAAATTTAAGC-CAGTTTAG
2910597 CTAGCACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.02
28 13 0.30
29 5 0.12
30 6 0.14
31 16 0.37
32 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (28 bp):
AAAATTTAAGCCAGTTTAGTTGGCAACC
Found at i:2911248 original size:9 final size:8
Alignment explanation
Indices: 2911233--2911299 Score: 62
Period size: 9 Copynumber: 7.5 Consensus size: 8
2911223 CCATTAAACA
2911233 AAAAATAT
1 AAAAATAT
2911241 ACAAAATAT
1 A-AAAATAT
2911250 ACAAAATATTT
1 A-AAAATA--T
2911261 AAAAAATAT
1 -AAAAATAT
2911270 AAGAAATAT
1 AA-AAATAT
2911279 AAAAATAT
1 AAAAATAT
*
2911287 ATAAATAAT
1 AAAAAT-AT
2911296 AAAA
1 AAAA
2911300 GGGGAGCTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
8 14 0.27
9 29 0.57
11 7 0.14
12 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (8 bp):
AAAAATAT
Found at i:2911257 original size:18 final size:16
Alignment explanation
Indices: 2911233--2911299 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 16
2911223 CCATTAAACA
2911233 AAAAATATACAAAATAT
1 AAAAATATA-AAAATAT
2911250 ACAAAATATTTAAAAAATAT
1 A-AAAATA--T-AAAAATAT
2911270 AAGAAATATAAAAATAT
1 AA-AAATATAAAAATAT
*
2911287 ATAAATAATAAAA
1 AAAAAT-ATAAAA
2911300 GGGGAGCTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 4 0.09
17 16 0.37
18 7 0.16
19 1 0.02
20 14 0.33
21 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (16 bp):
AAAAATATAAAAATAT
Found at i:2911276 original size:29 final size:28
Alignment explanation
Indices: 2911232--2911296 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
2911222 GCCATTAAAC
*
2911232 AAAAAATATACAAAATATACAAAATATTT
1 AAAAAATATACAAAATATA-AAAATATAT
2911261 AAAAAATATA-AGAAATATAAAAATATAT
1 AAAAAATATACA-AAATATAAAAATATAT
*
2911289 AAATAATA
1 AAAAAATA
2911297 AAAGGGGAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAAAATATACAAAATATAAAAATATAT
Found at i:2911299 original size:17 final size:17
Alignment explanation
Indices: 2911235--2911287 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
2911225 ATTAAACAAA
2911235 AAATATACAAAATATACA-
1 AAATATA-AAAATATA-AG
2911253 AAATATTTAAAAAATATAAG
1 AAATA--T-AAAAATATAAG
2911273 AAATATAAAAATATA
1 AAATATAAAAATATA
2911288 TAAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 1 0.03
20 14 0.45
21 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATATAAAAATATAAG
Found at i:2912567 original size:19 final size:18
Alignment explanation
Indices: 2912543--2912597 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
2912533 GGGTTTCACC
2912543 AGGGTTTAGGGTTTCATTT
1 AGGGTTTA-GGTTTCATTT
* *
2912562 AGGGTTTCAAGTTTCACTT
1 AGGGTTT-AGGTTTCATTT
*
2912581 AAGGTTTAAGGTTTCAT
1 AGGGTTT-AGGTTTCAT
2912598 AAAAGGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (18 bp):
AGGGTTTAGGTTTCATTT
Found at i:2912626 original size:20 final size:20
Alignment explanation
Indices: 2912572--2912627 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2912562 AGGGTTTCAA
* *
2912572 GTTTCA-CTTAAGGTTTAAG
1 GTTTCATCTAAAGTTTTAAG
*
2912591 GTTTCAT-AAAAGGTTTTAAG
1 GTTTCATCTAAA-GTTTTAAG
2912611 GTTTCATCTAAAGTTTT
1 GTTTCATCTAAAGTTTT
2912628 GGGTTTCACT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (20 bp):
GTTTCATCTAAAGTTTTAAG
Found at i:2915256 original size:8 final size:8
Alignment explanation
Indices: 2915243--2915298 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
2915233 AAAGATGAAA
2915243 TTTTTTT-
1 TTTTTTTG
2915250 TTTTTTTG
1 TTTTTTTG
*
2915258 GTTTTTTG
1 TTTTTTTG
*
2915266 TTTGTTTG
1 TTTTTTTG
*
2915274 TTTGTGTT-
1 TTT-TTTTG
2915282 TTTTTTT-
1 TTTTTTTG
2915289 TTTTTTTG
1 TTTTTTTG
2915297 TT
1 TT
2915299 AAGCTAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 17 0.43
8 21 0.52
9 2 0.05
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:2915643 original size:140 final size:140
Alignment explanation
Indices: 2915391--2915756 Score: 332
Period size: 140 Copynumber: 2.6 Consensus size: 140
2915381 AACTGAAAAT
* * *
2915391 AAATATGACT-AGTACTAAACCATAAGTC-GAAAAATAAAGGATGACT-GAATTGAGCTACAAGT
1 AAATATGACTAAG-ACTAAACCATAAGTCAG-AAAATAAA-GATAATTGGGATTGAGCTACAAGT
* * * * ** *
2915453 CAAAAAATAAAGATGATCGGGACTGAGTCACAAATTAAGGAATATAGATGA-TCAGGATTAAACC
63 TAAAAAATAAGGATGATCGGGACTGAATCACAAATCAAAAAATATAGATGACT-AGAATTAAACC
*
2915517 ACAAGTC-AGGAAAC
127 ACAAGTCAAAG-AAC
*
2915531 AAATATGACTAAGACTAAATCATAAGTCAGAAAATAAAGATAATTGGGATTGAGCTACAAGTTAA
1 AAATATGACTAAGACTAAACCATAAGTCAGAAAATAAAGATAATTGGGATTGAGCTACAAGTTAA
* ** * * * *
2915596 AAAATAAGGATGA-CGGAGATTGAATCGTAAGTCAAAAAATA-AGGATGACTATAATTGAACCAT
66 AAAATAAGGATGATCGG-GACTGAATCACAAATCAAAAAATATA-GATGACTAGAATTAAACCAC
* * *
2915659 AGGTTAAAGAAT
129 AAGTCAAAGAAC
* * * * * * **
2915671 ATAGATGACCAAGACTAAACCATAAGTCAAAAAATAAAAATAATAGGGATTGAGCCGCAAGTTAA
1 AAATATGACTAAGACTAAACCATAAGTCAGAAAATAAAGATAATTGGGATTGAGCTACAAGTTAA
* *
2915736 GAAATAAGGATGATCGAGACT
66 AAAATAAGGATGATCGGGACT
2915757 AAGCAGCAAA
Statistics
Matches: 184, Mismatches: 34, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
139 9 0.05
140 167 0.91
141 8 0.04
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.21
Consensus pattern (140 bp):
AAATATGACTAAGACTAAACCATAAGTCAGAAAATAAAGATAATTGGGATTGAGCTACAAGTTAA
AAAATAAGGATGATCGGGACTGAATCACAAATCAAAAAATATAGATGACTAGAATTAAACCACAA
GTCAAAGAAC
Found at i:2915723 original size:70 final size:70
Alignment explanation
Indices: 2915535--2915758 Score: 200
Period size: 70 Copynumber: 3.2 Consensus size: 70
2915525 GGAAACAAAT
* * * * *
2915535 ATGACTAAGACTAAATCATAAGTCAGAAAATAAAGATAATTGGGATTGAGCTACAAGTTAAAAAA
1 ATGACCAAGACTAAATCATAAGTCAAAAAATAAAGATAATAGGGATTGAACCACAAGTTAAAAAA
2915600 TAAGG
66 TAAGG
** * * * * * ** * * *
2915605 ATGACGGAGATTGAATCGTAAGTCAAAAAATAAGGATGACTA-TAATTGAACCATAGGTTAAAGA
1 ATGACCAAGACTAAATCATAAGTCAAAAAATAAAGAT-AATAGGGATTGAACCACAAGTTAAAAA
2915669 ATATA-G
65 ATA-AGG
* * * * *
2915675 ATGACCAAGACTAAACCATAAGTCAAAAAATAAAAATAATAGGGATTGAGCCGCAAGTTAAGAAA
1 ATGACCAAGACTAAATCATAAGTCAAAAAATAAAGATAATAGGGATTGAACCACAAGTTAAAAAA
2915740 TAAGG
66 TAAGG
* *
2915745 ATGATCGAGACTAA
1 ATGACCAAGACTAA
2915759 GCAGCAAATT
Statistics
Matches: 115, Mismatches: 35, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
69 4 0.03
70 108 0.94
71 3 0.03
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (70 bp):
ATGACCAAGACTAAATCATAAGTCAAAAAATAAAGATAATAGGGATTGAACCACAAGTTAAAAAA
TAAGG
Found at i:2920427 original size:19 final size:18
Alignment explanation
Indices: 2920386--2920424 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2920376 TTTTGAAAAC
2920386 TTTATTTGAAAAGATTTT
1 TTTATTTGAAAAGATTTT
*
2920404 TTTATTTGAAAAGGTTTT
1 TTTATTTGAAAAGATTTT
2920422 TTT
1 TTT
2920425 TATAGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (18 bp):
TTTATTTGAAAAGATTTT
Found at i:2920860 original size:19 final size:19
Alignment explanation
Indices: 2920836--2920872 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2920826 TTTCTAGAAA
*
2920836 ATCCCACCCAAAAATTCAT
1 ATCCCACCAAAAAATTCAT
*
2920855 ATCCCATCAAAAAATTCA
1 ATCCCACCAAAAAATTCA
2920873 AACATTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (19 bp):
ATCCCACCAAAAAATTCAT
Found at i:2921500 original size:21 final size:21
Alignment explanation
Indices: 2921474--2921516 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2921464 AATAATAAAA
*
2921474 ATGGTCCAATTGACCCCGGAC
1 ATGGTCCAATCGACCCCGGAC
* *
2921495 ATGGTCCGATCGACCTCGGAC
1 ATGGTCCAATCGACCCCGGAC
2921516 A
1 A
2921517 CAAACGTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.19
Consensus pattern (21 bp):
ATGGTCCAATCGACCCCGGAC
Found at i:2922600 original size:18 final size:19
Alignment explanation
Indices: 2922577--2922615 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2922567 GCGATAATTA
2922577 AAGTTTA-ATTACAAA-AAT
1 AAGTTTAGATTA-AAACAAT
2922595 AAGTTTAGATTAAAACAAT
1 AAGTTTAGATTAAAACAAT
2922614 AA
1 AA
2922616 AATATCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (19 bp):
AAGTTTAGATTAAAACAAT
Found at i:2923266 original size:14 final size:15
Alignment explanation
Indices: 2923230--2923263 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2923220 GCAGCAGAAA
* *
2923230 AAAAAGAGAAACTAG
1 AAAAAGAAAAACCAG
2923245 AAAAAGAAAAACCAG
1 AAAAAGAAAAACCAG
2923260 AAAA
1 AAAA
2923264 GAACAACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAACCAG
Found at i:2923921 original size:2 final size:2
Alignment explanation
Indices: 2923914--2923939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2923904 AAGTTAAGGT
2923914 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2923940 AAGGGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2924123 original size:21 final size:18
Alignment explanation
Indices: 2924078--2924123 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 18
2924068 TTGGAGAATT
2924078 AAATAAAAATAAATAATA
1 AAATAAAAATAAATAATA
2924096 AATATAAAAATCCAAATAATA
1 AA-ATAAAAAT--AAATAATA
2924117 CAAATAA
1 -AAATAA
2924124 TAATGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
21 12 0.50
22 2 0.08
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAAAATAAATAATA
Found at i:2926473 original size:16 final size:16
Alignment explanation
Indices: 2926448--2926500 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
2926438 CTCTAATAAA
*
2926448 AATTTCTAAAAACTAT
1 AATTTTTAAAAACTAT
2926464 AATTTTTAAAAACTAT
1 AATTTTTAAAAACTAT
*
2926480 AATTATTAATAAA-TA-
1 AATTTTTAA-AAACTAT
2926495 AATTTT
1 AATTTT
2926501 GTAACTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 5 0.15
16 25 0.76
17 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTTTTAAAAACTAT
Found at i:2935257 original size:22 final size:24
Alignment explanation
Indices: 2935231--2935276 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
2935221 ATGTTGTATC
2935231 AATTACATTTTTTA-ATG-AATTT
1 AATTACATTTTTTACATGTAATTT
**
2935253 AATTATTTTTTTTACATGTAATTT
1 AATTACATTTTTTACATGTAATTT
2935277 TTCTATGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 3 0.15
24 5 0.25
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTACATTTTTTACATGTAATTT
Found at i:2937654 original size:331 final size:328
Alignment explanation
Indices: 2937019--2937665 Score: 1010
Period size: 331 Copynumber: 2.0 Consensus size: 328
2937009 TATTTGCCAT
* * * * *
2937019 AATCATTAAATTACACTATGATTTAAAACCTCTTCTTTTTTCCTTGAAAATGCTTTCTTGCCTTT
1 AATCATTAAATTACACTATAATTTAAAACCTCTACTTTTTCCCTTGAAAAGGCTTTCTTACCTTT
* * *
2937084 TTTCTTTTTCCTTTGAGAAAGCTTTCTTATGATGTTAGCATGCTTTATAGTTGTAGACTTGAACG
66 TTTCTTTTTCCTTTGAGAAAGATTCCTTATGATGTAAGCATGCTTTATAGTTGTAGACTTGAACG
* *
2937149 TTATAGTGAAAATATTTGTTTAATGATGTTCTGTTGACTAAAACAATCTTAGGTTGGTTTCATTA
131 TTATAGTGAAAATATTTGTTTAATGATGTTCTATTGACTAAAACAATCATAGGTTGGTTTCATTA
* **
2937214 AGTTATTATTTGGAATTAAACTAAAGGAATGAGGAGATTACACATGTAAATTAGGCTATTTCTGG
196 AGTTATTATTTGGAATTAAACTAAAAGAATGAGGAGATTACACATACAAATTAGGCTATTTCTGG
* *
2937279 TTCGTTCATGCATTACACTAATGAATAAGATGTTTATAAAATTATTTTTGCTGGTATCATCTTTG
261 TTCATTCATGCATTACACTAATAAATAAGATGTTTATAAAATTA-TTTTGCTGGTATCATCTTTG
2937344 ATAA
325 ATAA
*
2937348 AATCATTAAATTACACTATAATTTAAAGCCTGC-ACTTTTTCCCTTGAAAAGGCTTTCTTACCTT
1 AATCATTAAATTACACTATAATTTAAAACCT-CTACTTTTTCCCTTGAAAAGGCTTTCTTACCTT
* * * *
2937412 TTTTCTTTTTCCTTTGAGAAGGATTCCTTTTGATGTAAGCATGCTTTGTAGTTGTAGACTTGAAT
65 TTTTCTTTTTCCTTTGAGAAAGATTCCTTATGATGTAAGCATGCTTTATAGTTGTAGACTTGAAC
2937477 GTTATAGTGAAAAATATTTGTTTAATGATAGTTCTATTGACTAAAACAATCATAGGTTGGTTTCA
130 GTTATAGTG-AAAATATTTGTTTAATGAT-GTTCTATTGACTAAAACAATCATAGGTTGGTTTCA
* *
2937542 TTAAGTTATTATTTGGAATTAAACTAAAAGAAT-AGGGAGATTGCACATACAAATTAGGTTATTT
193 TTAAGTTATTATTTGGAATTAAACTAAAAGAATGA-GGAGATTACACATACAAATTAGGCTATTT
* * *
2937606 TTGGTTCATTCATGCATTACACTAATAAATAGGATGTTTATAAAATTATTTTGTTGGTAT
257 CTGGTTCATTCATGCATTACACTAATAAATAAGATGTTTATAAAATTATTTTGCTGGTAT
2937666 ATAAATGGAT
Statistics
Matches: 289, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
329 123 0.43
330 32 0.11
331 134 0.46
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (328 bp):
AATCATTAAATTACACTATAATTTAAAACCTCTACTTTTTCCCTTGAAAAGGCTTTCTTACCTTT
TTTCTTTTTCCTTTGAGAAAGATTCCTTATGATGTAAGCATGCTTTATAGTTGTAGACTTGAACG
TTATAGTGAAAATATTTGTTTAATGATGTTCTATTGACTAAAACAATCATAGGTTGGTTTCATTA
AGTTATTATTTGGAATTAAACTAAAAGAATGAGGAGATTACACATACAAATTAGGCTATTTCTGG
TTCATTCATGCATTACACTAATAAATAAGATGTTTATAAAATTATTTTGCTGGTATCATCTTTGA
TAA
Found at i:2937918 original size:15 final size:15
Alignment explanation
Indices: 2937900--2937935 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2937890 TTTGTAGACA
*
2937900 TTTAATGATGTTTGT
1 TTTAATGATGTTTAT
*
2937915 TTTATTGATGTTTAT
1 TTTAATGATGTTTAT
2937930 TTTAAT
1 TTTAAT
2937936 AGACTTGGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (15 bp):
TTTAATGATGTTTAT
Found at i:2938279 original size:55 final size:54
Alignment explanation
Indices: 2938209--2938349 Score: 173
Period size: 54 Copynumber: 2.6 Consensus size: 54
2938199 CGTCAATAAA
* *
2938209 ATATA-ATAAAAAATAAAAACATATAAGTCTATACTTACAGTCTCTAGCTGTC-
1 ATATAGATAAAAAATAAAAACATATAAGTCTATACTTACAGTCTCTAACCGTCG
*
2938261 AGTATAGATAAGAAAATAAAAACATATAAGT-TATACTTATAGTCTCTAACCGTCG
1 A-TATAGATAA-AAAATAAAAACATATAAGTCTATACTTACAGTCTCTAACCGTCG
* *
2938316 ATATAGGTAAAAAAATTAAAAA-ATACAAGTCTAT
1 ATATAGAT-AAAAAA-TAAAAACATATAAGTCTAT
2938350 GGTGAACAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
52 1 0.01
53 4 0.05
54 41 0.53
55 31 0.40
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (54 bp):
ATATAGATAAAAAATAAAAACATATAAGTCTATACTTACAGTCTCTAACCGTCG
Found at i:2938470 original size:56 final size:56
Alignment explanation
Indices: 2938390--2938564 Score: 183
Period size: 56 Copynumber: 3.2 Consensus size: 56
2938380 AAAAAATTAT
** * * **
2938390 AAGTCTATATTGACGGGTGTTAACCGTTGGTATTGGTAAGAAAAATTAAAATATGT
1 AAGTCTATATTGACGGGCATTAACCATTGGTATTGGTAAGAAAAATTAAAACATAC
* * ** * *
2938446 AAGTCTATATTGATGGGCACTAACCATCAGTA-TAG-AAAAAAAATTAAAACATAC
1 AAGTCTATATTGACGGGCATTAACCATTGGTATTGGTAAGAAAAATTAAAACATAC
* * * * *
2938500 AAGTCTATACTGACGAGCTTTAAGCATTGGTATAGGTAAGAAAAATTAAAACATAC
1 AAGTCTATATTGACGGGCATTAACCATTGGTATTGGTAAGAAAAATTAAAACATAC
2938556 AAGTCTATA
1 AAGTCTATA
2938565 CTAATACATG
Statistics
Matches: 94, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
54 39 0.41
55 3 0.03
56 52 0.55
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (56 bp):
AAGTCTATATTGACGGGCATTAACCATTGGTATTGGTAAGAAAAATTAAAACATAC
Found at i:2938507 original size:54 final size:56
Alignment explanation
Indices: 2938419--2938566 Score: 156
Period size: 54 Copynumber: 2.7 Consensus size: 56
2938409 TTAACCGTTG
* * * ** * * *
2938419 GTATTGGTAAGAAAAATTAAAATATGTAAGTCTATATTGATGGGCACTAACCATCA
1 GTATAGGTAAAAAAAATTAAAACATACAAGTCTATACTGACGAGCACTAACCATCA
** * **
2938475 GTATA-G-AAAAAAAATTAAAACATACAAGTCTATACTGACGAGCTTTAAGCATTG
1 GTATAGGTAAAAAAAATTAAAACATACAAGTCTATACTGACGAGCACTAACCATCA
*
2938529 GTATAGGTAAGAAAAATTAAAACATACAAGTCTATACT
1 GTATAGGTAAAAAAAATTAAAACATACAAGTCTATACT
2938567 AATACATGTT
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 41 0.54
55 2 0.03
56 33 0.43
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (56 bp):
GTATAGGTAAAAAAAATTAAAACATACAAGTCTATACTGACGAGCACTAACCATCA
Found at i:2947630 original size:15 final size:15
Alignment explanation
Indices: 2947609--2947652 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2947599 GGCAAGTAAG
2947609 AAAATGCAAGAAAAT
1 AAAATGCAAGAAAAT
*
2947624 GAAATGC-AGAAAAGT
1 AAAATGCAAGAAAA-T
2947639 AAAATGCAA-AAAAT
1 AAAATGCAAGAAAAT
2947653 TAAAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 7 0.28
15 17 0.68
16 1 0.04
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.14
Consensus pattern (15 bp):
AAAATGCAAGAAAAT
Found at i:2952168 original size:17 final size:17
Alignment explanation
Indices: 2952146--2952179 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2952136 TTCTTCAAGA
*
2952146 TTGCATTAACTCAACTT
1 TTGCATCAACTCAACTT
2952163 TTGCATCAACTCAACTT
1 TTGCATCAACTCAACTT
2952180 CTCAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (17 bp):
TTGCATCAACTCAACTT
Found at i:2957564 original size:21 final size:21
Alignment explanation
Indices: 2957539--2957580 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2957529 GCATAAGACT
*
2957539 ATAAAAAATCTGGAAAATATA
1 ATAAAAAATCTAGAAAATATA
2957560 ATAAAAAATCTAGAAAATATA
1 ATAAAAAATCTAGAAAATATA
2957581 GGAACAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (21 bp):
ATAAAAAATCTAGAAAATATA
Found at i:2957589 original size:21 final size:21
Alignment explanation
Indices: 2957541--2957589 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2957531 ATAAGACTAT
* *
2957541 AAAAAATCTGGAAAATATAAT
1 AAAAAATCTAGAAAATATAAG
*
2957562 AAAAAATCTAGAAAATATAGG
1 AAAAAATCTAGAAAATATAAG
*
2957583 AACAAAT
1 AAAAAAT
2957590 ATGTATAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.20
Consensus pattern (21 bp):
AAAAAATCTAGAAAATATAAG
Found at i:2959365 original size:13 final size:14
Alignment explanation
Indices: 2959347--2959379 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2959337 TACCAGAAAC
*
2959347 AAAAATAATAC-AA
1 AAAAATAAAACTAA
2959360 AAAAATAAAACTAA
1 AAAAATAAAACTAA
2959374 AAAAAT
1 AAAAAT
2959380 CTAATGGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAAACTAA
Found at i:2960769 original size:18 final size:18
Alignment explanation
Indices: 2960741--2960782 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2960731 TTGGGTTTAA
2960741 GTTTAGGGTTTAGGGGTTG
1 GTTT-GGGTTTAGGGGTTG
*
2960760 GTTTGGGTTTAGGGTTTG
1 GTTTGGGTTTAGGGGTTG
2960778 GTTTG
1 GTTTG
2960783 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.07, C:0.00, G:0.45, T:0.48
Consensus pattern (18 bp):
GTTTGGGTTTAGGGGTTG
Found at i:2960787 original size:17 final size:18
Alignment explanation
Indices: 2960749--2960850 Score: 70
Period size: 18 Copynumber: 5.7 Consensus size: 18
2960739 AAGTTTAGGG
* *
2960749 TTTAGGGGTTGGTTTGGG
1 TTTAGGGTTTGGTTTGGA
2960767 TTTAGGGTTTGGTTT-GA
1 TTTAGGGTTTGGTTTGGA
* *
2960784 TTTAGGGTTTAGTTTAAGA
1 TTTAGGGTTTGGTTT-GGA
*
2960803 TTT-GAGGTTCGGTTTAGGGA
1 TTTAG-GGTTTGGTTT--GGA
2960823 -TT-GGGTTTGGGTTTGG-
1 TTTAGGGTTT-GGTTTGGA
*
2960839 TTTAAGGTTTGG
1 TTTAGGGTTTGG
2960851 GAATTGGTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
17 21 0.31
18 24 0.35
19 21 0.31
20 2 0.03
ACGTcount: A:0.13, C:0.01, G:0.39, T:0.47
Consensus pattern (18 bp):
TTTAGGGTTTGGTTTGGA
Found at i:2960835 original size:24 final size:25
Alignment explanation
Indices: 2960803--2960851 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2960793 TAGTTTAAGA
*
2960803 TTTGAGGTTCGGTTTAGGGATTGGG
1 TTTGAGGTTCGGTTTAAGGATTGGG
* *
2960828 TTTG-GGTTTGGTTTAAGGTTTGGG
1 TTTGAGGTTCGGTTTAAGGATTGGG
2960852 AATTGGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.10, C:0.02, G:0.43, T:0.45
Consensus pattern (25 bp):
TTTGAGGTTCGGTTTAAGGATTGGG
Found at i:2960848 original size:31 final size:32
Alignment explanation
Indices: 2960813--2960891 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
2960803 TTTGAGGTTC
2960813 GGTTTAGGGATTGGGTTTGG-GTTT-GGTTTAA
1 GGTTTAGGGATTGGGTTTGGAGTTTAGGTTT-A
* *
2960844 GGTTT-GGGAATTGGTTTTGGATTTTAGGTTTA
1 GGTTTAGGG-ATTGGGTTTGGAGTTTAGGTTTA
*
2960876 -GTTTAGGGTTTGGGTT
1 GGTTTAGGGATTGGGTT
2960892 CAGTTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 3 0.08
31 25 0.62
32 7 0.17
33 5 0.12
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (32 bp):
GGTTTAGGGATTGGGTTTGGAGTTTAGGTTTA
Found at i:2961105 original size:20 final size:20
Alignment explanation
Indices: 2961060--2961126 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
2961050 TCTAGGTTAT
* *
2961060 GGTTTAAAGGTTTAAGTTTAG
1 GGTTTGAAGGTTTAA-TTTGG
*
2961081 GGTTTGAGGGTTTAATTTGG
1 GGTTTGAAGGTTTAATTTGG
* *
2961101 GGTTTAAAGGTTTGATTTGG
1 GGTTTGAAGGTTTAATTTGG
2961121 GGTTTG
1 GGTTTG
2961127 GAGTTTAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (20 bp):
GGTTTGAAGGTTTAATTTGG
Found at i:2961146 original size:67 final size:68
Alignment explanation
Indices: 2961061--2961194 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 68
2961051 CTAGGTTATG
* *
2961061 GTTTAAAGGTTTAAGTTTAGGGTTTGAGGGTTTAATTTGGGGTTTAAAGGTTTGATTTGGGGTTT
1 GTTTAAAGGTTTAAGTTTAGAGTTTGAGGGTTTAATTTGGGGTTTAAAGATTTGATTTGGGGTTT
2961126 GGA
66 GGA
* ** * *
2961129 GTTTAAA-GTTTAGGTTTAGAGTTTGAGGGTTTGGTTTGGGGTTTGAAGATTTGGTTTGGGGTTT
1 GTTTAAAGGTTTAAGTTTAGAGTTTGAGGGTTTAATTTGGGGTTTAAAGATTTGATTTGGGGTTT
2961193 GG
66 GG
2961195 TTTAGGGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
67 52 0.88
68 7 0.12
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (68 bp):
GTTTAAAGGTTTAAGTTTAGAGTTTGAGGGTTTAATTTGGGGTTTAAAGATTTGATTTGGGGTTT
GGA
Found at i:2961152 original size:27 final size:27
Alignment explanation
Indices: 2961089--2961153 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
2961079 AGGGTTTGAG
*
2961089 GGTTTA-A-TTTGGGGTTTAAAGGTTT
1 GGTTTAGAGTTTGGAGTTTAAAGGTTT
* * *
2961114 GATTTGGGGTTTGGAGTTTAAA-GTTT
1 GGTTTAGAGTTTGGAGTTTAAAGGTTT
2961140 AGGTTTAGAGTTTG
1 -GGTTTAGAGTTTG
2961154 AGGGTTTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 22 0.73
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (27 bp):
GGTTTAGAGTTTGGAGTTTAAAGGTTT
Found at i:2961193 original size:20 final size:19
Alignment explanation
Indices: 2961121--2961193 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
2961111 TTTGATTTGG
*
2961121 GGTTTGGAGTTTAAAGTTT
1 GGTTTGGAGTTTGAAGTTT
* *
2961140 AGGTTTAGAGTTTGAGGGTTT
1 -GGTTTGGAGTTTGA-AGTTT
*
2961161 GGTTTGGGGTTTGAAGATTT
1 GGTTTGGAGTTTGAAG-TTT
*
2961181 GGTTTGGGGTTTG
1 GGTTTGGAGTTTG
2961194 GTTTAGGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.89
21 4 0.09
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (19 bp):
GGTTTGGAGTTTGAAGTTT
Found at i:2961205 original size:19 final size:19
Alignment explanation
Indices: 2961068--2961244 Score: 71
Period size: 20 Copynumber: 8.9 Consensus size: 19
2961058 ATGGTTTAAA
2961068 GGTTTAAGTTTAGGGTTTGAG
1 GGTTT-AGTTTAGGGTTTG-G
* * **
2961089 GGTTTAATTTGGGGTTTAAA
1 GGTTTAGTTTAGGGTTT-GG
*
2961109 GGTTT-GATTTGGGGTTTGG
1 GGTTTAG-TTTAGGGTTTGG
* *
2961128 AGTTTAAAGTTTA-GGTTTAG
1 GGTTT--AGTTTAGGGTTTGG
*
2961148 AGTTTGAGGGTTT--GGTTTGG
1 GGTTT-A--GTTTAGGGTTTGG
2961168 GGTTTGAAGATTT--GGTTTGG
1 GGTTT--AG-TTTAGGGTTTGG
*
2961188 GGTTTGGTTTAGGGTTTGG
1 GGTTTAGTTTAGGGTTTGG
* * *
2961207 GATTTAGATTA-GGTTTAAG
1 GGTTTAGTTTAGGGTTT-GG
2961226 GGTTTAAGTTTAGGGTTTG
1 GGTTT-AGTTTAGGGTTTG
2961245 ACGATTTAAG
Statistics
Matches: 120, Mismatches: 22, Indels: 29
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.03
18 6 0.05
19 26 0.22
20 66 0.55
21 18 0.15
22 1 0.01
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (19 bp):
GGTTTAGTTTAGGGTTTGG
Found at i:2963732 original size:23 final size:23
Alignment explanation
Indices: 2963700--2963750 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
2963690 TGTGGGTTTC
2963700 TTTTTCTTAAAATT-TTCCTTTTTA
1 TTTTTCTT-AAATTCTTCC-TTTTA
*
2963724 TTTTT-TTAATTTCTTCCTTTTA
1 TTTTTCTTAAATTCTTCCTTTTA
2963746 TTTTT
1 TTTTT
2963751 ATTGATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 14 0.56
23 6 0.24
24 5 0.20
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTCTTAAATTCTTCCTTTTA
Found at i:2964760 original size:5 final size:5
Alignment explanation
Indices: 2964750--2964775 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2964740 ATAACCCATT
2964750 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
2964776 AGGTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:2965110 original size:13 final size:14
Alignment explanation
Indices: 2965074--2965110 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2965064 ATATAGATAT
*
2965074 TAAA-AAAAAATTA
1 TAAATAAAAAATCA
2965087 TAAATAAAAAATCA
1 TAAATAAAAAATCA
2965101 -AAATAAAAAA
1 TAAATAAAAAA
2965111 ATTTTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAATAAAAAATCA
Found at i:2965474 original size:17 final size:17
Alignment explanation
Indices: 2965452--2965485 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2965442 ATACTTTGCA
*
2965452 AAAGGAATTGCAAAATG
1 AAAGGAATTACAAAATG
2965469 AAAGGAATTACAAAATG
1 AAAGGAATTACAAAATG
2965486 CTAGAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (17 bp):
AAAGGAATTACAAAATG
Found at i:2968848 original size:3 final size:3
Alignment explanation
Indices: 2968827--2968866 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
2968817 TATAAATGAT
* *
2968827 TAA TAG TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2968867 TACTCTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2973688 original size:14 final size:15
Alignment explanation
Indices: 2973658--2973690 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2973648 AATAAATATT
2973658 AAAAATCATACCATGC
1 AAAAATCATA-CATGC
2973674 AAAAATCAT-CATGC
1 AAAAATCATACATGC
2973688 AAA
1 AAA
2973691 TATATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAAATCATACATGC
Done.