Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 70 of 168
Found at i:20526668 original size:18 final size:19
Alignment explanation
Indices: 20526631--20526667 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20526621 TTGTAAAAAA
*
20526631 TATAAAT-TTTGAAATTTT
1 TATAAATATTTTAAATTTT
20526649 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
20526668 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:20526677 original size:19 final size:20
Alignment explanation
Indices: 20526636--20526679 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
20526626 AAAAATATAA
*
20526636 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTTAAAAAT
20526656 ATTTT-AAA-TTTTAAAAATT
1 ATTTTGAAATTTTTAAAAA-T
20526675 ATTTT
1 ATTTT
20526680 TGAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAAAT
Found at i:20533066 original size:43 final size:43
Alignment explanation
Indices: 20533005--20533158 Score: 236
Period size: 43 Copynumber: 3.6 Consensus size: 43
20532995 TGTCCCAGAC
* ** * *
20533005 ATGGTCTTACATAGAAATCTCGTATCGATGCCAATAGCTCAACT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
20533049 ATGGTCTTACATGAAATCTCAAATCGATACCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
20533092 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
20533135 ATGGTCTTACACGAAATCTCAAAT
1 ATGGTCTTACACGAAATCTCAAAT
20533159 AGATATTGGA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
43 91 0.89
44 11 0.11
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:20535781 original size:21 final size:22
Alignment explanation
Indices: 20535739--20535781 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
20535729 TATACATTGA
*
20535739 TGTTTTAAATCCATAAGGTATTT
1 TGTTTTAAAT-CATAAGATATTT
*
20535762 TGTTTTAAAT-ATAATATATT
1 TGTTTTAAATCATAAGATATT
20535782 ATTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (22 bp):
TGTTTTAAATCATAAGATATTT
Found at i:20541079 original size:31 final size:30
Alignment explanation
Indices: 20541044--20541105 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
20541034 GTCAACAAAA
*
20541044 AAAAAGAGTAAAAA-ATGAAAAAGTGAAAATG
1 AAAAAGA--AAAAAGATGAAAAAGTAAAAATG
*
20541075 AAAAATAAAAAATGATGAAAAAGTAAAAATG
1 AAAAAGAAAAAA-GATGAAAAAGTAAAAATG
20541106 GAGAGGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
31 22 0.81
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.15
Consensus pattern (30 bp):
AAAAAGAAAAAAGATGAAAAAGTAAAAATG
Found at i:20541105 original size:17 final size:15
Alignment explanation
Indices: 20541045--20541103 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 15
20541035 TCAACAAAAA
20541045 AAAAGAGTAAAAAATG
1 AAAA-AGTAAAAAATG
*
20541061 AAAAAGT-GAAAATG
1 AAAAAGTAAAAAATG
20541075 AAAAA-TAAAAAATGATG
1 AAAAAGT-AAAAA--ATG
20541092 AAAAAGTAAAAA
1 AAAAAGTAAAAA
20541104 TGGAGAGGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 1 0.03
14 11 0.31
15 6 0.17
16 4 0.11
17 13 0.36
18 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.14
Consensus pattern (15 bp):
AAAAAGTAAAAAATG
Found at i:20542589 original size:129 final size:129
Alignment explanation
Indices: 20542359--20543105 Score: 1109
Period size: 129 Copynumber: 5.8 Consensus size: 129
20542349 AATATAGCAA
** *
20542359 ATCTTGTCTCCCTAAGCAGTTTCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGG
1 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
*
20542424 AAGCAGATTTAAGCCACAAGTCCTATATCACTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
66 AAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
** * *
20542488 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTAGGG
1 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
* * *
20542553 AAGCAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGCAGTGGAATATGTTGGGAAATGACAG
66 AAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
*
20542617 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATTTTATCTTCAAGAGTAAGG
1 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
* **
20542682 AAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGATTAAGAAATTACAG
66 AAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
*
20542746 ATCTTGTCTCCCTAAGTAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
1 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
*
20542811 AAGCAGATTTAAGCCACAAGGGCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
66 AAGCAGATTTAAGCCACAA-GTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
* ******* ** *
20542876 ATCTGGGGGAGAGAGAG-AGGGGTAGCAAAGCAGATCGGAGACGGCAAATCTTATCTTCAAGAGT
1 ATCTTGTCTCCCTA-AGCA---GTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGT
* *
20542940 AAGGAAGTAGATTTAAGCCACAAGTCCTATATCCCTGGTCATCAGTGGAATAGGTTGGGAAATTA
62 AAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
20543005 CAG
127 CAG
* * * **
20543008 ATCTTGTCTCCTTAAGCAATAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGG
1 ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
* *
20543073 AAGCAGATTTAAGCCACAAGTCTTATCTCCCTG
66 AAGCAGATTTAAGCCACAAGTCCTATATCCCTG
20543106 AAGGTGCAGT
Statistics
Matches: 552, Mismatches: 60, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
129 388 0.70
130 48 0.09
131 4 0.01
132 50 0.09
133 62 0.11
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (129 bp):
ATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGG
AAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAG
Found at i:20543118 original size:262 final size:257
Alignment explanation
Indices: 20542384--20543105 Score: 1086
Period size: 262 Copynumber: 2.8 Consensus size: 257
20542374 GCAGTTTCGG
*
20542384 AGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
1 AGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
*
20542449 TATCACTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
66 TATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
* *
20542514 GCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTAGGGAAGCAGATTTAAGCCACAAGTCTTAT
131 GCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCTTAT
* * * ** ** **
20542579 ATCCCTGGTCAGCAGTGGAATATGTTGGGAAATGACAGATCTTGTCTCCCTAAGCAGTAGCGG
196 ATCCCTGGT-AGCAGTGGAATAGGTTGGGAAATGACAGATCTGGGCGACAGAAGCAGTAGCAA
*
20542642 AGCAGATCGAAGACGGCAAATTTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
1 AGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
* ** *
20542707 TATCCCTGGTCAGCAGTGGAATAGATTAAGAAATTACAGATCTTGTCTCCCTAAGTAGTAGCGGA
66 TATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
** * *
20542772 GCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGGGCCTA
131 GCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAA-GTCTTA
* * *
20542837 TATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTGGGGGAGAGAGAG-AGGGGTAG
195 TATCCCTGGT-AGCAGTGGAATAGGTTGGGAAATGACAGATCTGGGCGACAGA-AGCA---GTAG
20542901 CAA
255 CAA
* *
20542904 AGCAGATCGGAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTCCTA
1 AGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
* * * *
20542969 TATCCCTGGTCATCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCTTAAGCAATAGTGGA
66 TATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
20543034 GCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCTTAT
131 GCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCTTAT
*
20543099 CTCCCTG
196 ATCCCTG
20543106 AAGGTGCAGT
Statistics
Matches: 418, Mismatches: 41, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
258 177 0.42
259 48 0.11
260 2 0.00
261 11 0.03
262 180 0.43
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (257 bp):
AGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
TATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
GCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCTTAT
ATCCCTGGTAGCAGTGGAATAGGTTGGGAAATGACAGATCTGGGCGACAGAAGCAGTAGCAA
Found at i:20544066 original size:16 final size:15
Alignment explanation
Indices: 20544047--20544086 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
20544037 TTTTTTATTT
*
20544047 TTTTGTTTTCTTTTTC
1 TTTTGTTTTC-CTTTC
20544063 TTTTGTTTTCCTTTC
1 TTTTGTTTTCCTTTC
20544078 TTTT-TTTTC
1 TTTTGTTTTC
20544087 ATGGTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTTGTTTTCCTTTC
Found at i:20548992 original size:20 final size:20
Alignment explanation
Indices: 20548967--20549007 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20548957 ATCAGCCTAT
*
20548967 CATCAATTATAAATTAGTTA
1 CATCAATTAGAAATTAGTTA
20548987 CATCAATTAGAAATTAGTTA
1 CATCAATTAGAAATTAGTTA
20549007 C
1 C
20549008 TAGAGTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
CATCAATTAGAAATTAGTTA
Found at i:20553369 original size:40 final size:40
Alignment explanation
Indices: 20553314--20553393 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
20553304 TGGAGAGGTG
* *
20553314 GTGTAATAAGGATTATGTAATAGTTATTATGAAAATGAGT
1 GTGTAATAAGGATTATGTAATAGTCATTATAAAAATGAGT
* * *
20553354 GTGTACTATGGATTATGTAATAGTCATTGTAAAAATGAGT
1 GTGTAATAAGGATTATGTAATAGTCATTATAAAAATGAGT
20553394 ATTTTCTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.38
Consensus pattern (40 bp):
GTGTAATAAGGATTATGTAATAGTCATTATAAAAATGAGT
Found at i:20554598 original size:23 final size:22
Alignment explanation
Indices: 20554572--20554615 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
20554562 TCCCTCTCTT
20554572 ACATGTTCTTCTCTTCTCTTTTC
1 ACATGTTCTTCT-TTCTCTTTTC
* * *
20554595 ACATTTTTTTCTTTTTCTTTT
1 ACATGTTCTTCTTTCTCTTTT
20554616 AATCTTTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (22 bp):
ACATGTTCTTCTTTCTCTTTTC
Found at i:20557580 original size:6 final size:6
Alignment explanation
Indices: 20557564--20557613 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
20557554 TATCGTCCCT
* * *
20557564 CCTCATC CCTCTC CCTCTC TCTCTC CCTC-C CTTTTC CCTCTC CCTCTC
1 CCTC-TC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
20557612 CC
1 CC
20557614 CACTTATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
5 3 0.08
6 29 0.81
7 4 0.11
ACGTcount: A:0.02, C:0.62, G:0.00, T:0.36
Consensus pattern (6 bp):
CCTCTC
Found at i:20557665 original size:25 final size:28
Alignment explanation
Indices: 20557637--20557696 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 28
20557627 TGACTCAACA
*
20557637 ATTTAATATTAATA-TAAT-T-ATTTTT
1 ATTTAATATTAATATTAATATAACTTTT
20557662 ATTTAATATTAATATTAATATAACTTTT
1 ATTTAATATTAATATTAATATAACTTTT
20557690 ATTTAAT
1 ATTTAAT
20557697 TCGATTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 14 0.45
26 4 0.13
27 1 0.03
28 12 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTAATATTAATATTAATATAACTTTT
Found at i:20585002 original size:7 final size:7
Alignment explanation
Indices: 20584990--20585014 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20584980 ATAGCCTAAT
20584990 ATATATA
1 ATATATA
20584997 ATATATA
1 ATATATA
20585004 ATATATA
1 ATATATA
20585011 ATAT
1 ATAT
20585015 TATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:20587873 original size:26 final size:27
Alignment explanation
Indices: 20587843--20587908 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
20587833 TTTTAAATTT
* *
20587843 TAAATAATATTCTTAATATATTATTAA
1 TAAATAATATTATTAATATATTAATAA
*
20587870 -AAAT-ATTTATATTAATATATTAATAA
1 TAAATAATAT-TATTAATATATTAATAA
20587896 TAAATATATATTA
1 TAAATA-ATATTA
20587909 CAATTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 3 0.10
26 19 0.61
27 4 0.13
28 2 0.06
29 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAATAATATTATTAATATATTAATAA
Found at i:20589197 original size:3 final size:3
Alignment explanation
Indices: 20589191--20589222 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20589181 GGAGGAGGAG
20589191 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
20589223 GAAAGCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20592115 original size:21 final size:22
Alignment explanation
Indices: 20592070--20592116 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
20592060 ATAAGGTCTA
* * *
20592070 TAGGCCGTTTTTATTTTTTATT
1 TAGGCCGATTTTATATTTTAAT
20592092 TAGGCCGATTTTA-ATTTTAAT
1 TAGGCCGATTTTATATTTTAAT
20592113 TAGG
1 TAGG
20592117 GAAATAGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (22 bp):
TAGGCCGATTTTATATTTTAAT
Found at i:20598278 original size:22 final size:21
Alignment explanation
Indices: 20598240--20598281 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
20598230 GTAACAATTT
*
20598240 AGATAAGATACAGAACATATC
1 AGATAAGATACAAAACATATC
*
20598261 AGATACAGATGCAAAACATAT
1 AGATA-AGATACAAAACATAT
20598282 TGGAATCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (21 bp):
AGATAAGATACAAAACATATC
Found at i:20609732 original size:5 final size:6
Alignment explanation
Indices: 20609714--20609741 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20609704 TAATTATTTT
20609714 AATAAA AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATA
20609742 TAATCAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:20609732 original size:43 final size:45
Alignment explanation
Indices: 20609649--20609735 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 45
20609639 CCAAATTAAA
*
20609649 TTTATAATATAAATTATTATTTATATAAAATAAAAATAAAAATAG
1 TTTATAATATAAATTATTATTAATATAAAATAAAAATAAAAATAG
* *
20609694 TTTATAATGTTAATTATT-TTAATA-AAAATAAAAATAAAAATA
1 TTTATAATATAAATTATTATTAATATAAAATAAAAATAAAAATA
20609736 AAAATATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 18 0.46
44 5 0.13
45 16 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (45 bp):
TTTATAATATAAATTATTATTAATATAAAATAAAAATAAAAATAG
Found at i:20609751 original size:42 final size:44
Alignment explanation
Indices: 20609660--20609752 Score: 102
Period size: 43 Copynumber: 2.1 Consensus size: 44
20609650 TTATAATATA
* *** *
20609660 AATTATTATTTATATAAAATAAAAATAAAAATAGTTTATAATGTT
1 AATTATTATTAATATAAAATAAAAATAAAAATAAAATATAA-GTC
20609705 AATTATT-TTAATA-AAAATAAAAATAAAAATAAAAATATAA-TC
1 AATTATTATTAATATAAAATAAAAATAAAAAT-AAAATATAAGTC
20609747 AATTAT
1 AATTAT
20609753 AAATCTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
42 7 0.17
43 17 0.40
44 11 0.26
45 7 0.17
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (44 bp):
AATTATTATTAATATAAAATAAAAATAAAAATAAAATATAAGTC
Found at i:20610275 original size:31 final size:27
Alignment explanation
Indices: 20610235--20610306 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 27
20610225 GTATCACTAC
*
20610235 AGAACAACTCTTATTTGGAACAACTATGTTG
1 AGAATAACTCTTATTTGGAAC-AC---GTTG
*
20610266 AGAATAACTCATATTTGGAACACGTTG
1 AGAATAACTCTTATTTGGAACACGTTG
20610293 -GAATAACTCTTATT
1 AGAATAACTCTTATT
20610307 CAAAGCAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 13 0.34
27 4 0.11
30 2 0.05
31 19 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
AGAATAACTCTTATTTGGAACACGTTG
Found at i:20610520 original size:28 final size:28
Alignment explanation
Indices: 20610480--20610536 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
20610470 AATATGAAGA
20610480 TAGTTAATAAGTTTTCCTCTTAACTTTT
1 TAGTTAATAAGTTTTCCTCTTAACTTTT
*
20610508 TAGTTAATAAGTTTTTCTCTTAACTTTT
1 TAGTTAATAAGTTTTCCTCTTAACTTTT
20610536 T
1 T
20610537 CCTGAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.56
Consensus pattern (28 bp):
TAGTTAATAAGTTTTCCTCTTAACTTTT
Found at i:20612266 original size:6 final size:6
Alignment explanation
Indices: 20612255--20612375 Score: 242
Period size: 6 Copynumber: 20.2 Consensus size: 6
20612245 TATATATATT
20612255 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
20612303 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
20612351 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
20612376 ACAAATGTTT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 115 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:20615598 original size:4 final size:4
Alignment explanation
Indices: 20615589--20615654 Score: 132
Period size: 4 Copynumber: 16.5 Consensus size: 4
20615579 GAGGCACCAA
20615589 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
20615637 TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TA
20615655 AGTCCCGCTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:20616417 original size:11 final size:11
Alignment explanation
Indices: 20616403--20616443 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
20616393 TAAACTCTCT
20616403 TTAAAGTTTTG
1 TTAAAGTTTTG
*
20616414 TTAAAATTTT-
1 TTAAAGTTTTG
*
20616424 TTAAGGTTTTG
1 TTAAAGTTTTG
20616435 TT-AAGTTTT
1 TTAAAGTTTT
20616444 CATGAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (11 bp):
TTAAAGTTTTG
Found at i:20621404 original size:41 final size:41
Alignment explanation
Indices: 20621352--20621497 Score: 175
Period size: 41 Copynumber: 3.6 Consensus size: 41
20621342 ACAAATTCAA
* * *
20621352 CGGCACATAGCCCGCTAGACTTATAGCCTGATTCAGATCAC
1 CGGCACGTAGCCTGCTAGACTTATAACCTGATTCAGATCAC
* **
20621393 CGGTACGTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
1 CGGCACGTAGCCTGCTAGACTTATAACCTGATTCAGATCAC
* * **
20621434 CGGCACGCAGCCTACTAGGTTTATAACCTGATTCAGATCAC
1 CGGCACGTAGCCTGCTAGACTTATAACCTGATTCAGATCAC
* **
20621475 TGGCAATTAGCCTGCTAGACTTA
1 CGGCACGTAGCCTGCTAGACTTA
20621498 AAGTCTGAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (41 bp):
CGGCACGTAGCCTGCTAGACTTATAACCTGATTCAGATCAC
Found at i:20631075 original size:2 final size:2
Alignment explanation
Indices: 20631068--20631104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20631058 CACCCGCATG
20631068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20631105 ATGGTGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20631369 original size:19 final size:19
Alignment explanation
Indices: 20631345--20631383 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20631335 TATATATTCA
*
20631345 TATAGAATGTCGTAAAATT
1 TATAGAATGACGTAAAATT
*
20631364 TATAGAATGACGTGAAATT
1 TATAGAATGACGTAAAATT
20631383 T
1 T
20631384 GTTTGATTCA
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:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (19 bp):
TATAGAATGACGTAAAATT
Found at i:20643595 original size:28 final size:28
Alignment explanation
Indices: 20643573--20643667 Score: 145
Period size: 28 Copynumber: 3.4 Consensus size: 28
20643563 CTTCATGTAT
*
20643573 GAGTCCGCGTGGACTATCTTTCAAGCAA
1 GAGTCCGCATGGACTATCTTTCAAGCAA
* * * *
20643601 GAGTTCGTATAGACTATCTTTCAACCAA
1 GAGTCCGCATGGACTATCTTTCAAGCAA
20643629 GAGTCCGCATGGACTATCTTTCAAGCAA
1 GAGTCCGCATGGACTATCTTTCAAGCAA
20643657 GAGTCCGCATG
1 GAGTCCGCATG
20643668 AGCTAACTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.26
Consensus pattern (28 bp):
GAGTCCGCATGGACTATCTTTCAAGCAA
Found at i:20643884 original size:28 final size:28
Alignment explanation
Indices: 20643825--20643886 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
20643815 AATCTGCCTT
** *
20643825 TATGAATCTGTAACTATGATTCAACATG
1 TATGAATCTGTAACTATGAACCAACATA
* **
20643853 TATGAATCTGTACCTATGAACCCGCATA
1 TATGAATCTGTAACTATGAACCAACATA
20643881 TATGAA
1 TATGAA
20643887 ATCATTTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (28 bp):
TATGAATCTGTAACTATGAACCAACATA
Found at i:20645644 original size:16 final size:17
Alignment explanation
Indices: 20645618--20645653 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20645608 TCAGAATCAG
*
20645618 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
20645635 ATTG-GAAAATTAATTA
1 ATTGAGAAAATTAATTA
20645651 ATT
1 ATT
20645654 TCTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:20652514 original size:43 final size:41
Alignment explanation
Indices: 20652457--20652700 Score: 166
Period size: 43 Copynumber: 5.7 Consensus size: 41
20652447 CATACTGACT
* *
20652457 CATA-AGTGTATCATCGGATGAACCAACACAATTATATTGGTA
1 CATATAGTGCATCATCGGAT-AACCAA-AGAATTATATTGGTA
** * *
20652499 CATATAGTGCATCATCGGATATACTGAAGAATTATACTGGCA
1 CATATAGTGCATCATCGGATA-ACCAAAGAATTATATTGGTA
* * *
20652541 CATACAGTGCATCATCGGATAAACCAAAGTATCTATATTAGTA
1 CATATAGTGCATCATCGGAT-AACCAAAGAAT-TATATTGGTA
* * * * *
20652584 CATATAGTGCATCATTGGATATACCGAAGAAAATATACTGGCA
1 CATATAGTGCATCATCGGATA-ACCAAAG-AATTATATTGGTA
* * * ** * * *
20652627 CACATAGTGTATCATCAGATAAACTGAAGAAAATATATCGGCA
1 CATATAGTGCATCATCGGAT-AACCAAAG-AATTATATTGGTA
* * *
20652670 CACACAGTGCATCATCGGATAAACCGAAGAA
1 CATATAGTGCATCATCGGAT-AACCAAAGAA
20652701 AATATACTGG
Statistics
Matches: 163, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
42 46 0.28
43 115 0.71
44 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (41 bp):
CATATAGTGCATCATCGGATAACCAAAGAATTATATTGGTA
Found at i:20652679 original size:86 final size:86
Alignment explanation
Indices: 20652504--20652822 Score: 363
Period size: 86 Copynumber: 3.7 Consensus size: 86
20652494 TGGTACATAT
* * * * *
20652504 AGTGCATCATCGGATATACTGAAG-AATTATACTGGCACATACAGTGCATCATCGGATAAACCAA
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAGATAAACCAA
* ** * * * *
20652568 AGTATCTATATTAGTACATAT
66 AGAAAATATATCAGCACACAC
* * * * **
20652589 AGTGCATCATTGGATATACCGAAGAAAATATACTGGCACACATAGTGTATCATCAGATAAACTGA
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAGATAAACCAA
*
20652654 AGAAAATATATCGGCACACAC
66 AGAAAATATATCAGCACACAC
* *
20652675 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACACAATACATCATC-GAATAAACCA
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAG-ATAAACCA
*
20652739 AAGAAAATATACCAGCACACAC
65 AAGAAAATATATCAGCACACAC
* * * * * *
20652761 AATGCATCATCAGATAAATCGAAGTAAATATACTAGCACATACAGTGCATCATCAGATAAAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAGATAAAC
20652823 AGAAGTATAA
Statistics
Matches: 196, Mismatches: 35, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
85 23 0.12
86 172 0.88
87 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (86 bp):
AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAGATAAACCAA
AGAAAATATATCAGCACACAC
Found at i:20652701 original size:43 final size:43
Alignment explanation
Indices: 20652504--20652827 Score: 328
Period size: 43 Copynumber: 7.6 Consensus size: 43
20652494 TGGTACATAT
* * * *
20652504 AGTGCATCATCGGATATACTGAAG-AATTATACTGGCACATAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
* * ** * * * * *
20652546 AGTGCATCATCGGATAAACCAAAGTATCTATATTAGTACATAT
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
* * *
20652589 AGTGCATCATTGGATATACCGAAGAAAATATACTGGCACACAT
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
* * *
20652632 AGTGTATCATCAGATAAACTGAAGAAAATATA-TCGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATACT-GGCACACAC
20652675 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
* * * * **
20652718 AATACATCATCGAATAAACCAAAGAAAATATACCAGCACACAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
* * * * * *
20652761 AATGCATCATCAGATAAATCGAAGTAAATATACTAGCACATAC
1 AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
* *
20652804 AGTGCATCATCAGATAAACAGAAG
1 AGTGCATCATCGGATAAACCGAAG
20652828 TATAACCTGT
Statistics
Matches: 234, Mismatches: 45, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
42 22 0.09
43 211 0.90
44 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (43 bp):
AGTGCATCATCGGATAAACCGAAGAAAATATACTGGCACACAC
Found at i:20656060 original size:70 final size:69
Alignment explanation
Indices: 20655986--20656238 Score: 292
Period size: 70 Copynumber: 3.6 Consensus size: 69
20655976 GTTTTAGATC
* * ** * * * *
20655986 GGACAACCAATGATTCAAATCACAACATTAGCATTTTAATCATCTAAATACCAT-AATTATGCCC
1 GGACAGCCAATGATTCAAAT-ATAACAACAGCATTTTAATTAGCTAAACACCATGAATT-TGTCC
20656050 TAATTT
64 TAATTT
* * *
20656056 GGACAGCCAATGATTCACATTATAACAACAACATTTTCATTAGCTAAACACCATGAATTTGTCCT
1 GGACAGCCAATGATTCA-AATATAACAACAGCATTTTAATTAGCTAAACACCATGAATTTGTCCT
20656121 AATTT
65 AATTT
* *
20656126 GGACAGCCAATGATTTACAATATAACAACAGCATATTAATTAGCTAAACACCATGAATTTGTCCT
1 GGACAGCCAATGATTCA-AATATAACAACAGCATTTTAATTAGCTAAACACCATGAATTTGTCCT
20656191 AATTT
65 AATTT
* * * * *
20656196 GGATAGCCAATGATTTACAATATAATAGCAGCATATTAATTAG
1 GGACAGCCAATGATTCA-AATATAACAACAGCATTTTAATTAG
20656239 TAATAAATTG
Statistics
Matches: 162, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
70 156 0.96
71 6 0.04
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (69 bp):
GGACAGCCAATGATTCAAATATAACAACAGCATTTTAATTAGCTAAACACCATGAATTTGTCCTA
ATTT
Found at i:20662156 original size:12 final size:12
Alignment explanation
Indices: 20662139--20662182 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
20662129 TGGCTTCTAT
20662139 GCAGACCATGAA
1 GCAGACCATGAA
20662151 GCAGACCATGAA
1 GCAGACCATGAA
20662163 GCAGACCATGAA
1 GCAGACCATGAA
20662175 GCAGACCA
1 GCAGACCA
20662183 AGCTGCCCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.25, T:0.07
Consensus pattern (12 bp):
GCAGACCATGAA
Found at i:20668053 original size:47 final size:45
Alignment explanation
Indices: 20668002--20668169 Score: 123
Period size: 47 Copynumber: 3.6 Consensus size: 45
20667992 TATTTAATAT
*
20668002 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
20668049 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* * **
20668093 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTG
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
20668140 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
20668170 TTTTAATTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 26
0.70 0.10 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.13
46 10 0.11
47 35 0.37
48 9 0.10
49 5 0.05
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:20668075 original size:91 final size:91
Alignment explanation
Indices: 20667928--20668135 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 91
20667918 TTGATTTTAG
* *
20667928 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
20667993 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
20668020 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
20668085 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
20668111 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
20668136 GTTGTAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 89 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:20668096 original size:44 final size:43
Alignment explanation
Indices: 20667949--20668110 Score: 116
Period size: 44 Copynumber: 3.6 Consensus size: 43
20667939 AAGAACATTT
* * *
20667949 TATTATTAAGAATT-TTATGAAATTATATATCATTATTAAATTA
1 TATTAATAATAATTATT-TGAAATTATATATAATTATTAAATTA
* * * *
20667992 TATTTAATATTAATTATTTTAAATTGTATA-AATTCATATAAGA-AA
1 TA-TTAATAATAATTATTTGAAATTATATATAATT-AT-TAA-ATTA
* *
20668037 AATTATTATCAATAATT-TTATGAAATTATATATTATTATTAAATTA
1 TATTA--AT-AATAATTATT-TGAAATTATATATAATTATTAAATTA
*
20668083 TATGTAATAATAATTATTTTAAATTATA
1 TAT-TAATAATAATTATTTGAAATTATA
20668111 CAAATTCATA
Statistics
Matches: 91, Mismatches: 15, Indels: 25
0.69 0.11 0.19
Matches are distributed among these distances:
43 5 0.05
44 40 0.44
45 12 0.13
46 11 0.12
47 20 0.22
48 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (43 bp):
TATTAATAATAATTATTTGAAATTATATATAATTATTAAATTA
Found at i:20668110 original size:26 final size:28
Alignment explanation
Indices: 20667948--20668024 Score: 52
Period size: 28 Copynumber: 2.8 Consensus size: 28
20667938 TAAGAACATT
* *
20667948 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
* ** *
20667978 TCATTATTAAATTATATTTAATATTA-A
1 TTATTATTAAATTATATGAAATAATATA
*
20668005 TTATT-TTAAATTGTAT-AAAT
1 TTATTATTAAATTATATGAAAT
20668025 TCATATAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.08
26 10 0.26
27 5 0.13
28 12 0.32
29 1 0.03
30 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:20668317 original size:25 final size:26
Alignment explanation
Indices: 20668285--20668339 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
20668275 TTATTAAATT
*
20668285 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
20668310 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
20668335 A-ATAT
1 ATATAT
20668340 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:20668506 original size:39 final size:40
Alignment explanation
Indices: 20668463--20668567 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
20668453 TTCCATTATG
20668463 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
20668502 CTATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTA-TTC----CATTCAACCAAACACAAGATTTA
20668547 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
20668568 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 13 0.24
40 7 0.13
44 19 0.35
45 15 0.28
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:20668561 original size:45 final size:44
Alignment explanation
Indices: 20668461--20668570 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
20668451 TTTTCCATTA
20668461 TGCTATTACACCTCTA-TTC----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTTCATTACATTCAACCAAACACAAGAT
* * ***
20668500 TACTATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTTCATTACATTCAACCAAACACAAGA-T
*
20668545 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTTCATTACA
20668571 CCTCTATTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 14 0.25
40 3 0.05
44 16 0.28
45 24 0.42
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTTCATTACATTCAACCAAACACAAGAT
Found at i:20668570 original size:16 final size:16
Alignment explanation
Indices: 20668549--20668629 Score: 91
Period size: 16 Copynumber: 5.4 Consensus size: 16
20668539 TTGATTTGCT
20668549 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
20668565 ATTACACCTCTATT-C
1 ATTACACCTCTATTCC
20668580 ----CACCTCTATTCC
1 ATTACACCTCTATTCC
*
20668592 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
* *
20668608 AATACACCTCTAATCC
1 ATTACACCTCTATTCC
*
20668624 AATACA
1 ATTACA
20668630 GCGAACCAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
11 10 0.17
12 1 0.02
15 1 0.02
16 46 0.79
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:20668585 original size:27 final size:27
Alignment explanation
Indices: 20668547--20668608 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
20668537 AGTTGATTTG
*
20668547 CTATTACACCTCTATTCCATTACACCT
1 CTATTCCACCTCTATTCCATTACACCT
20668574 CTATTCCACCTCTATTCCATTACACCT
1 CTATTCCACCTCTATTCCATTACACCT
*
20668601 CTAATCCA
1 CTATTCCA
20668609 ATACACCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (27 bp):
CTATTCCACCTCTATTCCATTACACCT
Found at i:20669133 original size:18 final size:17
Alignment explanation
Indices: 20669112--20669146 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20669102 TTATTATTAA
*
20669112 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20669130 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20669147 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20669250 original size:18 final size:17
Alignment explanation
Indices: 20669227--20669263 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
20669217 AACTATTATT
20669227 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
20669243 AAATATATGATTTAATA
1 AAATATATGATTTAATA
20669260 AAAT
1 AAAT
20669264 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:20669412 original size:18 final size:17
Alignment explanation
Indices: 20669389--20669425 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
20669379 AAATATTATT
20669389 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
20669405 AAATATATGATTTAATA
1 AAATATATGATTTAATA
20669422 AAAT
1 AAAT
20669426 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:20669461 original size:47 final size:46
Alignment explanation
Indices: 20669408--20669648 Score: 175
Period size: 47 Copynumber: 5.3 Consensus size: 46
20669398 TTAATTAAAA
*
20669408 TATATG-ATTTAATAAAATTTAAAATAATTATTACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT
* **
20669455 TATATGAATTTTTATAATTTAAAATAATTATTATTAAATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTATTA-T-AATA-AATTTTCT
* *
20669503 TA-AT-AA-TT-TATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
* *
20669546 TATATGAATTTATATAATTTAAAATAATTA--ATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * * *
20669591 TA-AT-AATGATATATAATTTCATAA-AATTCTTAATAATAAATATTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
20669637 TATATGAATTTA
1 TATATGAATTTA
20669649 CTAAAATCAT
Statistics
Matches: 153, Mismatches: 20, Indels: 42
0.71 0.09 0.20
Matches are distributed among these distances:
42 2 0.01
43 12 0.08
44 41 0.27
45 16 0.10
46 11 0.07
47 53 0.35
48 16 0.10
49 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT
Found at i:20669515 original size:44 final size:44
Alignment explanation
Indices: 20669465--20669609 Score: 136
Period size: 44 Copynumber: 3.2 Consensus size: 44
20669455 TATATGAATT
20669465 TTTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAA
1 TTTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAA
* * **
20669509 TTTATAATTTCATAA-AATTCTTGA-T-AATA-AATTTTCTTATATGAA
1 TTTATAATTT-AAAATAATTATT-ATTAAATATAA-TTTAATA-AT-AA
* *
20669554 TTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
1 -TT-TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAA
*
20669600 TATATAATTT
1 TTTATAATTT
20669610 CATAAAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
42 2 0.03
43 9 0.11
44 27 0.34
45 7 0.09
46 7 0.09
47 16 0.20
48 9 0.11
49 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (44 bp):
TTTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAA
Found at i:20669516 original size:18 final size:17
Alignment explanation
Indices: 20669493--20669527 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20669483 TATTATTAAA
20669493 TATAATTTAATAATAATT
1 TATAATTTAATAA-AATT
*
20669511 TATAATTTCATAAAATT
1 TATAATTTAATAAAATT
20669528 CTTGATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATTTAATAAAATT
Found at i:20669544 original size:91 final size:91
Alignment explanation
Indices: 20669433--20669648 Score: 360
Period size: 91 Copynumber: 2.4 Consensus size: 91
20669423 AATTTAAAAT
* * * *
20669433 AATTATTACTAATAAATTTTCTTATATGAATTTTTATAATTTAAAATAATTATTATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
*
20669498 TTTAATAATAATTTATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
20669524 AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
*
20669589 TTTAATAATGATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
20669615 AATTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTA
20669649 CTAAAATCAT
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 116 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (91 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:20674486 original size:16 final size:16
Alignment explanation
Indices: 20674465--20674497 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20674455 GATACAATAT
*
20674465 AACAAAGGATAAGCAA
1 AACAAAGGATAACCAA
20674481 AACAAAGGATAACCAA
1 AACAAAGGATAACCAA
20674497 A
1 A
20674498 GTAACATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.15, G:0.15, T:0.06
Consensus pattern (16 bp):
AACAAAGGATAACCAA
Found at i:20685944 original size:15 final size:14
Alignment explanation
Indices: 20685903--20685944 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
20685893 TAATTTTTAA
20685903 TATTTTATTTTA-T
1 TATTTTATTTTATT
20685916 TATTTTAGTTTTATT
1 TATTTTA-TTTTATT
*
20685931 TCTCTTTATTTTAT
1 TAT-TTTATTTTAT
20685945 AATATTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 9 0.36
16 4 0.16
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:20698728 original size:2 final size:2
Alignment explanation
Indices: 20698721--20698745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20698711 AACAGAGGGT
20698721 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
20698746 AGGAGCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20703445 original size:31 final size:31
Alignment explanation
Indices: 20703398--20703456 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
20703388 ATCAACACTA
* * *
20703398 TTGTTATATACTTTTATTATTTTAGTCATTG
1 TTGTTACATACATTTATCATTTTAGTCATTG
20703429 TTGTTACATACATTTATCATTTTAGTCA
1 TTGTTACATACATTTATCATTTTAGTCA
20703457 CCCGTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.56
Consensus pattern (31 bp):
TTGTTACATACATTTATCATTTTAGTCATTG
Found at i:20703814 original size:12 final size:12
Alignment explanation
Indices: 20703797--20703826 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20703787 TCCTCTTACC
*
20703797 AGAAAAAGGAAA
1 AGAAAAAAGAAA
20703809 AGAAAAAAGAAA
1 AGAAAAAAGAAA
20703821 AGAAAA
1 AGAAAA
20703827 GATAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:20705341 original size:20 final size:20
Alignment explanation
Indices: 20705316--20705375 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
20705306 AATTTATTTC
*
20705316 ATCTTGGACTTTTCTAAGTG
1 ATCTTGGACTTTTCTAAGTA
* *
20705336 ATCTTGTA-TTATTCTAAATA
1 ATCTTGGACTT-TTCTAAGTA
* *
20705356 ATCTTCGACTTTTTTAAGTA
1 ATCTTGGACTTTTCTAAGTA
20705376 TGTTTTATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (20 bp):
ATCTTGGACTTTTCTAAGTA
Found at i:20713682 original size:2 final size:2
Alignment explanation
Indices: 20713675--20713702 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20713665 ATTGAAATGA
20713675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20713703 GTAGTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20715280 original size:57 final size:57
Alignment explanation
Indices: 20715211--20715323 Score: 140
Period size: 61 Copynumber: 1.9 Consensus size: 57
20715201 GTACTAAGAT
* *
20715211 TTTGCAAATAAAT-AGT-GATTCCAATACAATGCAGTTAGCTACCAAAAAGGTTAATA
1 TTTGCAAATAAATGAGTGGATTCCAATACAATGCACTTAGCAACC-AAAAGGTTAATA
* *
20715267 TTTGACAAATAAATGGGTGGAGATTCTAATACAATGCACTTAGCAACCAAAAGGTTA
1 TTTG-CAAATAAATGAGT-G-GATTCCAATACAATGCACTTAGCAACCAAAAGGTTA
20715324 TGACTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 4 0.08
57 9 0.19
58 2 0.04
60 9 0.19
61 24 0.50
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (57 bp):
TTTGCAAATAAATGAGTGGATTCCAATACAATGCACTTAGCAACCAAAAGGTTAATA
Found at i:20715281 original size:112 final size:110
Alignment explanation
Indices: 20715060--20715263 Score: 241
Period size: 112 Copynumber: 1.8 Consensus size: 110
20715050 TTGATACACT
* * *
20715060 AATACAATTACCATGGTGATTCCAATACAATACTAAGATTTTGCAAATGAATGGTGGTGATTCCG
1 AATACAATTACCATGGTGATTCCAATACAATACTAAGATTTTGCAAATGAA-GATAGTGATTCCA
** * * * * *
20715125 ATGTAGTGCACTTAGCCACTAAAATGTTATGAATTTTCTAAAATGTC
65 ATACAATGCACTTAGCCACAAAAAGGTTAT-AATTTACAAAAATGTC
* *
20715172 AATACAATTACCATGGTGATTCTAATACAGTACTAAGATTTTGCAAAT-AA-ATAGTGATTCCAA
1 AATACAATTACCATGGTGATTCCAATACAATACTAAGATTTTGCAAATGAAGATAGTGATTCCAA
* *
20715235 TACAATGCAGTTAGCTACCAAAAAGGTTA
66 TACAATGCACTTAGCCA-CAAAAAGGTTA
20715264 ATATTTGACA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
109 22 0.28
110 9 0.11
111 2 0.03
112 46 0.58
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (110 bp):
AATACAATTACCATGGTGATTCCAATACAATACTAAGATTTTGCAAATGAAGATAGTGATTCCAA
TACAATGCACTTAGCCACAAAAAGGTTATAATTTACAAAAATGTC
Found at i:20716426 original size:22 final size:22
Alignment explanation
Indices: 20716363--20716428 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
20716353 TATTGTTCAA
* *
20716363 ACATGAGAGCTTAGTACGTGAA
1 ACATGAGAGCTTAGTACGTTAG
20716385 ACATGAGAGCTTAGTACGTTAG
1 ACATGAGAGCTTAGTACGTTAG
*
20716407 CCATGAGAGCTTAGTACGTTAG
1 ACATGAGAGCTTAGTACGTTAG
20716429 TACTATTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (22 bp):
ACATGAGAGCTTAGTACGTTAG
Found at i:20719108 original size:31 final size:29
Alignment explanation
Indices: 20719073--20719155 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
20719063 ATAATATGAA
*
20719073 ATTATAAATAAAATTTGATTTAATGTCTAAT
1 ATTATAAATAAAATTTGATTT--TGTATAAT
* * *
20719104 ATTATATATGAATTTTGATTTTGTATAAT
1 ATTATAAATAAAATTTGATTTTGTATAAT
* *
20719133 TTTATAAGTGAAAATTT-ATTTTG
1 ATTATAAAT-AAAATTTGATTTTG
20719156 ATTCAATTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 19 0.45
30 5 0.12
31 18 0.43
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.51
Consensus pattern (29 bp):
ATTATAAATAAAATTTGATTTTGTATAAT
Found at i:20720310 original size:19 final size:19
Alignment explanation
Indices: 20720265--20720325 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
20720255 ATCTAATTAC
20720265 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TA-ATTT
*
20720286 AAATATTTAAATATAATTT
1 AAATATTTAATTATAATTT
*
20720305 ATATATTCTAATTA-AATTT
1 AAATATT-TAATTATAATTT
20720324 AA
1 AA
20720326 TAAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 7 0.20
21 12 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATAATTT
Found at i:20728895 original size:2 final size:2
Alignment explanation
Indices: 20728890--20728928 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20728880 AATAAAATTA
20728890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20728929 CTTAGTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20734584 original size:30 final size:30
Alignment explanation
Indices: 20734550--20734625 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
20734540 ACAAAAATAC
20734550 AAATTACATTTT-AGCCCCTAAACTTTTCAA
1 AAATTACATTTTGA-CCCCTAAACTTTTCAA
* *
20734580 AAATTACATTTTGACCCCTAACCTTTTCTA
1 AAATTACATTTTGACCCCTAAACTTTTCAA
* *
20734610 AATTTACATATTGACC
1 AAATTACATTTTGACC
20734626 TTTAATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTAAACTTTTCAA
Found at i:20735265 original size:15 final size:15
Alignment explanation
Indices: 20735241--20735290 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
20735231 CCAGAAGAAG
20735241 AAGAAA-AAGAAAAA
1 AAGAAAGAAGAAAAA
20735255 AAGAAAGAAGAAAAA
1 AAGAAAGAAGAAAAA
*
20735270 GAGAGAAG-AGAAAAA
1 AAGA-AAGAAGAAAAA
*
20735285 GAGAAA
1 AAGAAA
20735291 AAATATCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 8 0.24
15 22 0.67
16 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAGAAAAA
Found at i:20735270 original size:13 final size:13
Alignment explanation
Indices: 20735235--20735283 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
20735225 GTTCGGCCAG
*
20735235 AAGAAGAAGAA-A
1 AAGAAGAAAAAGA
20735247 AAGAA-AAAAAGA
1 AAGAAGAAAAAGA
20735259 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
*
20735272 GAGAAGAGAAAA
1 AAGAAGA-AAAA
20735284 AGAGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 4 0.12
12 11 0.34
13 13 0.41
14 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:20735286 original size:21 final size:20
Alignment explanation
Indices: 20735235--20735291 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
20735225 GTTCGGCCAG
*
20735235 AAGAAGAAGAAAAAGAAAAA
1 AAGAAAAAGAAAAAGAAAAA
*
20735255 AAGAAAGAAGAAAAAGAGAGAA
1 AAGAAA-AAGAAAAAGA-AAAA
*
20735277 GAGAAAAAGAGAAAA
1 AAGAAAAAGA-AAAA
20735292 AATATCACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 5 0.16
21 14 0.45
22 12 0.39
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAAAAGAAAAA
Found at i:20735287 original size:13 final size:12
Alignment explanation
Indices: 20735236--20735293 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
20735226 TTCGGCCAGA
20735236 AGAAGAAGAAAA-
1 AGAAGAA-AAAAG
*
20735248 AGAA-AAAAAGAA
1 AGAAGAAAAA-AG
20735260 AGAAGAAAAAGAG
1 AGAAGAAAAA-AG
20735273 AGAAGAGAAAAAG
1 AGAAGA-AAAAAG
20735286 AGAA-AAAA
1 AGAAGAAAA
20735294 TATCACAGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
10 3 0.07
11 6 0.15
12 9 0.22
13 19 0.46
14 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAAG
Found at i:20735290 original size:30 final size:27
Alignment explanation
Indices: 20735233--20735286 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
20735223 GAGTTCGGCC
*
20735233 AGAAGAAGAAGAAAAAGAAAAAAAGAA
1 AGAAGAAAAAGAAAAAGAAAAAAAGAA
* *
20735260 AGAAGAAAAAGAGAGAAGAGAAAAAGA
1 AGAAGAAAAAGA-AAAAGAAAAAAAGA
20735287 GAAAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (27 bp):
AGAAGAAAAAGAAAAAGAAAAAAAGAA
Found at i:20735391 original size:32 final size:33
Alignment explanation
Indices: 20735350--20735415 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
20735340 CAGCAGCCCC
*
20735350 AAAACAGCAGGCTTGTC-CAG-AAAAAAAACAAA
1 AAAACAGCAGGCCTG-CACAGAAAAAAAAACAAA
*
20735382 AAAATAGCAGGCCTGCAGCAGAAAAAAAAACAAA
1 AAAACAGCAGGCCTGCA-CAGAAAAAAAAACAAA
20735416 GCAGGCCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.03
32 13 0.45
33 3 0.10
34 12 0.41
ACGTcount: A:0.58, C:0.18, G:0.17, T:0.08
Consensus pattern (33 bp):
AAAACAGCAGGCCTGCACAGAAAAAAAAACAAA
Found at i:20735483 original size:20 final size:20
Alignment explanation
Indices: 20735460--20735497 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20735450 GCAGCTCTAG
20735460 CAGGCCAGCTCCAGCAGCCC
1 CAGGCCAGCTCCAGCAGCCC
* *
20735480 CAGGCCCGTTCCAGCAGC
1 CAGGCCAGCTCCAGCAGC
20735498 AGTCTAGCAT
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:0.18, C:0.47, G:0.26, T:0.08
Consensus pattern (20 bp):
CAGGCCAGCTCCAGCAGCCC
Found at i:20735612 original size:10 final size:9
Alignment explanation
Indices: 20735584--20735620 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
20735574 CCCAATCTGT
20735584 AGAAAAAAA
1 AGAAAAAAA
*
20735593 AGAAGAAAA
1 AGAAAAAAA
20735602 AGAAAAGAAA
1 AGAAAA-AAA
20735612 AGAAAAAAA
1 AGAAAAAAA
20735621 CAAAAAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:20735626 original size:19 final size:18
Alignment explanation
Indices: 20735586--20735627 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20735576 CAATCTGTAG
20735586 AAAAAAAAGAAGAAAAAGA
1 AAAAAAAAGAAGAAAAA-A
*
20735605 AAAGAAAAGAA-AAAAACA
1 AAAAAAAAGAAGAAAAA-A
20735623 AAAAA
1 AAAAA
20735628 GTCCCGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAGAAAAAA
Found at i:20736153 original size:36 final size:34
Alignment explanation
Indices: 20736111--20736454 Score: 169
Period size: 39 Copynumber: 9.3 Consensus size: 34
20736101 CGATACGTCT
*
20736111 TTTCAAAAATTTTCGTGTTTAAAAAATTTCTTGTG
1 TTTCAAAAATTTTCGTGTTTAAAAAATTT-TCGTG
*
20736146 TTTTCAAAAAAATTCTT-GTGTTT-AAAAATTTTCGTA
1 -TTTC--AAAAATT-TTCGTGTTTAAAAAATTTTCGTG
* * *
20736182 TTTCAAAACTTTTCATGTTTTCAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTG-TTT-AAAAAATTTTCGTG
* *
20736218 TTT-AAAAATTTTTTGCGT-TTTCAAAAATTTTTAGTG
1 TTTCAAAAA--TTTT-CGTGTTT-AAAAAATTTTCGTG
* * *
20736254 TTTCAAAAATTTTCGCGTTTTCAAAATAAAAATTTCATG
1 TTTCAAAAATTTTCGTG-TTT---AA-AAAATTTTCGTG
*
20736293 TTTCAAAGAA-TTTCGTGTTTTCAAAAAAAAGTTCTCGTG
1 TTTCAAA-AATTTTCGTG-TTT---AAAAAA-TTTTCGTG
** *
20736332 TTT-AAAAATTTTCGTGTTTTCAAAAAAAAAAGTTCTTG
1 TTTCAAAAATTTTCGTG-TTT----AAAAAATTTTCGTG
* * *
20736370 TTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTG
1 TTTCAAAAATTTTCGTG-TTT-AAAAAATTTTCGTG
* * *
20736406 TTTCCAAAAAAATTCTCGTGTTTCAAAAATTTCCGTG
1 TTT-C--AAAAATTTTCGTGTTTAAAAAATTTTCGTG
20736443 TTTTCAAAAATT
1 -TTTCAAAAATT
20736455 ATTATGGTGT
Statistics
Matches: 245, Mismatches: 38, Indels: 51
0.73 0.11 0.15
Matches are distributed among these distances:
32 2 0.01
33 8 0.03
34 5 0.02
35 19 0.08
36 55 0.22
37 31 0.13
38 48 0.20
39 75 0.31
40 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (34 bp):
TTTCAAAAATTTTCGTGTTTAAAAAATTTTCGTG
Found at i:20736266 original size:18 final size:18
Alignment explanation
Indices: 20736111--20736503 Score: 154
Period size: 18 Copynumber: 21.3 Consensus size: 18
20736101 CGATACGTCT
20736111 TTTCAAAAA-TTTTCGTG
1 TTTCAAAAATTTTTCGTG
*
20736128 TTTAAAAAATTTCTT-GTG
1 TTTCAAAAATTT-TTCGTG
*
20736146 TTTTCAAAAAAATTCTT-GTG
1 -TTTC--AAAAATTTTTCGTG
*
20736166 TTT-AAAAA-TTTTCGTA
1 TTTCAAAAATTTTTCGTG
* *
20736182 TTTC-AAAACTTTTCATG
1 TTTCAAAAATTTTTCGTG
* *
20736199 TTTTCAAAAAATTCTCGTG
1 -TTTCAAAAATTTTTCGTG
20736218 TTT-AAAAATTTTTTGCGT-
1 TTTCAAAAA-TTTTT-CGTG
*
20736236 TTTCAAAAATTTTTAGTG
1 TTTCAAAAATTTTTCGTG
*
20736254 TTTCAAAAA-TTTTCGCG
1 TTTCAAAAATTTTTCGTG
** *
20736271 TTTTCAAAATAAAAATTTCATG
1 -TTTC--AA-AAATTTTTCGTG
20736293 TTTCAAAGAA--TTTCGTG
1 TTTCAAA-AATTTTTCGTG
* *
20736310 TTTTCAAAAAAAAGTTCTCGTG
1 -TTTC---AAAAATTTTTCGTG
20736332 TTT-AAAAA-TTTTCGTG
1 TTTCAAAAATTTTTCGTG
*** *
20736348 TTTTCAAAAAAAAAAGTTCTTG
1 -TTTC---AAAAATTTTTCGTG
*
20736370 TTTC-AAAAGTTTTCGTG
1 TTTCAAAAATTTTTCGTG
** *
20736387 TTTTCAAAAAAGTTTAGTG
1 -TTTCAAAAATTTTTCGTG
* *
20736406 TTTCCAAAAAAATTCTCGTG
1 TTT-C-AAAAATTTTTCGTG
*
20736426 TTTCAAAAA-TTTCCGTG
1 TTTCAAAAATTTTTCGTG
*
20736443 TTTTCAAAAATTATTATGGTG
1 -TTTCAAAAATT-TT-TCGTG
*
20736464 TTTCAAAAA--TCTCGTG
1 TTTCAAAAATTTTTCGTG
* ** *
20736480 TTTTAAAAAAATATCGTG
1 TTTCAAAAATTTTTCGTG
20736498 TTTCAA
1 TTTCAA
20736504 TCGGATCACG
Statistics
Matches: 291, Mismatches: 43, Indels: 83
0.70 0.10 0.20
Matches are distributed among these distances:
15 3 0.01
16 33 0.11
17 57 0.20
18 73 0.25
19 43 0.15
20 34 0.12
21 32 0.11
22 16 0.05
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTCAAAAATTTTTCGTG
Found at i:20736307 original size:39 final size:38
Alignment explanation
Indices: 20736182--20736397 Score: 189
Period size: 39 Copynumber: 5.7 Consensus size: 38
20736172 AATTTTCGTA
* * *
20736182 TTTCAAAACTTTTCATGTTTTC---AAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAAATT-TCATG
* * * *
20736218 TTT-AAAAATTTTTTGCGTTTTC---AAAAATTTTTAGTG
1 TTTCAAAAA-TTTTCGTGTTTTCAAAAAAAAATTTCA-TG
*
20736254 TTTCAAAAATTTTCGCGTTTTCAAAATAAAAATTTCATG
1 TTTCAAAAATTTTCGTGTTTTCAAAA-AAAAATTTCATG
* *
20736293 TTTCAAAGAA-TTTCGTGTTTTCAAAAAAAAGTTCTCGTG
1 TTTCAAA-AATTTTCGTGTTTTCAAAAAAAAATT-TCATG
* *
20736332 TTT-AAAAATTTTCGTGTTTTCAAAAAAAAAAGTTCTTG
1 TTTCAAAAATTTTCGTGTTTTC-AAAAAAAAATTTCATG
*
20736370 TTTCAAAAGTTTTCGTGTTTTCAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAA
20736398 GTTTAGTGTT
Statistics
Matches: 151, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
35 5 0.03
36 37 0.25
37 7 0.05
38 34 0.23
39 58 0.38
40 10 0.07
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (38 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAAATTTCATG
Found at i:20736416 original size:77 final size:75
Alignment explanation
Indices: 20736216--20736434 Score: 237
Period size: 77 Copynumber: 2.9 Consensus size: 75
20736206 AAAATTCTCG
* * * * ** * *
20736216 TGTTTAAAAATTTTTTGCGTTTTCAAAAATTTTTAGTGTTTCAAAAATTTTCGCGTTTTCAAAAT
1 TGTTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
*
20736281 AAAAATTTCA
66 AAAAAGTTCA
* *
20736291 TGTTTC-AAAGAATTTCGTGTTTTCAAAAAAAAGTTCTCGTGTTT-AAAAATTTTCGTGTTTTCA
1 TGTTTCAAAAG-TTTTCGTGTTTTC--AAAAAAGTT-TAGTGTTTCAAAAATTTTCGTGTTTTCA
*
20736354 AAAAAAAAAGTTCT
62 AAAAAAAAAGTTCA
*
20736368 TGTTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTGTTTCCAAAAAAATTCTCGTG-TTTCAA
1 TGTTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTGTTT-C--AAAAATTTTCGTGTTTTCAA
20736432 AAA
63 AAA
20736435 TTTCCGTGTT
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
74 10 0.08
75 24 0.20
77 63 0.52
78 23 0.19
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (75 bp):
TGTTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
AAAAAGTTCA
Found at i:20736434 original size:37 final size:35
Alignment explanation
Indices: 20736382--20736503 Score: 120
Period size: 38 Copynumber: 3.3 Consensus size: 35
20736372 TCAAAAGTTT
* *
20736382 TCGTGTTTTCAAAAAAGTTTAGTGTTTCCAAAAAAATTC
1 TCGTG-TTTC-AAAAA-TTTCGTGTTT-CAAAAAAATTA
*
20736421 TCGTGTTTCAAAAATTTCCGTGTTTTCAAAAATTATTA
1 TCGTGTTTCAAAAATTT-CGTG-TTTCAAAAA-AATTA
* * *
20736459 TGGTGTTTCAAAAATCTCGTGTTTTAAAAAAA-TA
1 TCGTGTTTCAAAAATTTCGTGTTTCAAAAAAATTA
20736493 TCGTGTTTCAA
1 TCGTGTTTCAA
20736504 TCGGATCACG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
34 12 0.17
35 1 0.01
36 11 0.15
37 18 0.25
38 25 0.35
39 5 0.07
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (35 bp):
TCGTGTTTCAAAAATTTCGTGTTTCAAAAAAATTA
Found at i:20736472 original size:56 final size:54
Alignment explanation
Indices: 20736368--20736488 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 54
20736358 AAAAAGTTCT
* *
20736368 TGTTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTGTTTCCAAAAAAATTCTCG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAGTTTAGTGTTTCC-AAAAAA-TCTCG
*
20736424 TGTTTCAAAAATTTCCGTGTTTTCAAAAATTA-TTATGGTGTTT-C-AAAAATCTCG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAA--AGTT-TAGTGTTTCCAAAAAATCTCG
*
20736478 TGTTTTAAAAA
1 TGTTTCAAAAA
20736489 AATATCGTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
54 15 0.26
55 5 0.09
56 27 0.47
57 3 0.05
58 8 0.14
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (54 bp):
TGTTTCAAAAATTTCCGTGTTTTCAAAAAAGTTTAGTGTTTCCAAAAAATCTCG
Found at i:20737554 original size:4 final size:4
Alignment explanation
Indices: 20737545--20737569 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20737535 CGTTCATTGG
20737545 TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT T
20737570 GCATGTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:20742529 original size:75 final size:75
Alignment explanation
Indices: 20742405--20743084 Score: 946
Period size: 75 Copynumber: 9.1 Consensus size: 75
20742395 AGAATTATAT
* *
20742405 TTTTCAATTTCTGTTTGTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTTC-ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
20742470 ATCCTGAGGTA
65 ATCCTGAGGTA
*
20742481 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTTGGGTCACA
1 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
20742546 TCCTGAGGTA
66 TCCTGAGGTA
*
20742556 TTTTCATTTCTGTTTTTCAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
1 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
*
20742621 TCCTGAAGTA
66 TCCTGAGGTA
* *
20742631 TTTTCATTTCTGTTTTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCACA
1 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
20742696 TCCTGAGGTA
66 TCCTGAGGTA
*
20742706 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC-
1 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
*
20742770 -GCTGAGGTA
66 TCCTGAGGTA
** *
20742779 TTTTCAATTTCTACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTC-ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
20742844 CA--CTGAGGTA
64 CATCCTGAGGTA
* * * * *
20742854 TTTTCAATTTATGTTTTTCAAAAAATTAACTCATATTGTGAGAGGTGAGTTGAGCATCGGGCTGC
1 TTTTC-ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG-T-C
20742919 AC-TCC-GAGGTA
63 ACATCCTGAGGTA
* * * * *
20742930 TTTTTAATTTC--TTTTTAAAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCAC
1 -TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
*
20742993 ATGCTGAGGTATA
65 ATCCTGAGG--TA
* * * * * *
20743006 TTTTAATTTCTATTTTCCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCATTGGGTCATA
1 TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
20743071 TGCC-GAGGTA
66 T-CCTGAGGTA
20743081 TTTT
1 TTTT
20743085 TCAAAGGTCA
Statistics
Matches: 549, Mismatches: 40, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
72 3 0.01
73 16 0.03
74 96 0.17
75 358 0.65
76 20 0.04
77 55 0.10
78 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (75 bp):
TTTTCATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACA
TCCTGAGGTA
Found at i:20743471 original size:30 final size:30
Alignment explanation
Indices: 20743437--20743514 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
20743427 ACAAAAATAC
*
20743437 AAATTACATTTT-AGCCCCTAAACTTTTCAA
1 AAATTACATTTTGA-CCCCCAAACTTTTCAA
* *
20743467 AAATTACATTTTGACCCCCAACCTTTTCTA
1 AAATTACATTTTGACCCCCAAACTTTTCAA
* *
20743497 AATTTACATATTGACCCC
1 AAATTACATTTTGACCCC
20743515 TAATATTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 41 0.98
31 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTGACCCCCAAACTTTTCAA
Found at i:20743529 original size:30 final size:30
Alignment explanation
Indices: 20743460--20743530 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
20743450 GCCCCTAAAC
* * * *
20743460 TTTTCAAAAATTACATTTTGACCCCCAACC
1 TTTTCTAAATTTACATATTGACCCCCAACA
* *
20743490 TTTTCTAAATTTACATATTGACCCCTAATA
1 TTTTCTAAATTTACATATTGACCCCCAACA
*
20743520 TTTTGTAAATT
1 TTTTCTAAATT
20743531 ATATTTGGGC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTTCTAAATTTACATATTGACCCCCAACA
Found at i:20743927 original size:14 final size:14
Alignment explanation
Indices: 20743892--20743936 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
20743882 CGATCCCGCA
*
20743892 ACCACCATCGTCGC
1 ACCACCACCGTCGC
*
20743906 ACCGCCACCGT-GAC
1 ACCACCACCGTCG-C
20743920 ACCACCACCGTCGC
1 ACCACCACCGTCGC
20743934 ACC
1 ACC
20743937 TACACAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.22, C:0.53, G:0.16, T:0.09
Consensus pattern (14 bp):
ACCACCACCGTCGC
Found at i:20744137 original size:13 final size:13
Alignment explanation
Indices: 20744110--20744172 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
20744100 CGGCCCGAAG
*
20744110 AAGAAGAAAAA-A
1 AAGAAAAAAAAGA
20744122 AAGAAAAAAAAGA
1 AAGAAAAAAAAGA
20744135 AAGAAGAAAAAGAGA
1 AAGAA-AAAAA-AGA
*
20744150 CAAG-AAAAAGAGA
1 -AAGAAAAAAAAGA
*
20744163 GAGAAAAAAA
1 AAGAAAAAAA
20744173 TATCATAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
12 12 0.29
13 14 0.33
14 9 0.21
15 4 0.10
16 3 0.07
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:20744140 original size:25 final size:27
Alignment explanation
Indices: 20744110--20744172 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
20744100 CGGCCCGAAG
20744110 AAGAAGAAAAAAAAGA-AA-AAAAAGA
1 AAGAAGAAAAAAAAGACAAGAAAAAGA
*
20744135 AAGAAG-AAAAAGAGACAAGAAAAAGA
1 AAGAAGAAAAAAAAGACAAGAAAAAGA
*
20744161 GAG-AGAAAAAAA
1 AAGAAGAAAAAAA
20744173 TATCATAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 8 0.25
25 10 0.31
26 14 0.44
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (27 bp):
AAGAAGAAAAAAAAGACAAGAAAAAGA
Found at i:20744341 original size:17 final size:17
Alignment explanation
Indices: 20744321--20744386 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 17
20744311 CCAGCAGCTC
*
20744321 CAGCAGGCCAGCTCTAG
1 CAGCAGGCCAGCTCCAG
* *
20744338 CAGCCCCAGGCCTGTTCCAG
1 CAG---CAGGCCAGCTCCAG
20744358 CAGCAGGCCAGCATCCAG
1 CAGCAGGCCAGC-TCCAG
20744376 TCTAGCAGGCC
1 -C-AGCAGGCC
20744387 TAGTCCGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 10 0.26
18 5 0.13
19 1 0.03
20 22 0.58
ACGTcount: A:0.21, C:0.39, G:0.27, T:0.12
Consensus pattern (17 bp):
CAGCAGGCCAGCTCCAG
Found at i:20744992 original size:18 final size:17
Alignment explanation
Indices: 20744959--20745299 Score: 183
Period size: 17 Copynumber: 18.5 Consensus size: 17
20744949 CGATACATCT
20744959 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
20744976 TTTCAAAAATTTCTCGTG
1 TTTCAAAAATTT-TCGTG
20744994 TTTTCAAAAAAATTCTT-GTG
1 -TTTC--AAAAATT-TTCGTG
*
20745014 TTT-AAAAATTTTCGTA
1 TTTCAAAAATTTTCGTG
* *
20745030 TTTCAAAACTTTTCATG
1 TTTCAAAAATTTTCGTG
20745047 TTTTCAAAAAATTCTT-GTG
1 -TTTC-AAAAATT-TTCGTG
*
20745066 TTT-AAAAATTTTTCGCG
1 TTTCAAAAA-TTTTCGTG
*
20745083 TTTTCAAAAAATTTTTGGTG
1 -TTTC-AAAAA-TTTTCGTG
20745103 TTTCAAAAATTTTCGCAT-
1 TTTCAAAAATTTTCG--TG
*
20745121 TTTCAAAATTTTTTTCGTG
1 TTTCAAAA--ATTTTCGTG
20745140 TTTCAAAGAA-TTTCGTG
1 TTTCAAA-AATTTTCGTG
** *
20745157 TTTTCAAAAAAAAAAAGTTCTTG
1 -TTTC-----AAAAATTTTCGTG
*
20745180 TTTCAAAAGTTTTCGTG
1 TTTCAAAAATTTTCGTG
* *
20745197 TTTTCAAAAAAGTTTAGTG
1 -TTTC-AAAAATTTTCGTG
*
20745216 TTTCCAAAAAAATTCTCGTG
1 TTT-C--AAAAATTTTCGTG
*
20745236 TTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
*
20745253 TTTTCAGAAAATTATTATGGTG
1 -TTTCA-AAAA-T-TT-TCGTG
*
20745275 TTTCAAAAA-TCTCGTG
1 TTTCAAAAATTTTCGTG
*
20745291 TTTTAAAAA
1 TTTCAAAAA
20745300 AAATATCATG
Statistics
Matches: 256, Mismatches: 31, Indels: 75
0.71 0.09 0.21
Matches are distributed among these distances:
15 2 0.01
16 31 0.12
17 59 0.23
18 45 0.18
19 43 0.17
20 43 0.17
21 15 0.06
22 10 0.04
23 8 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:20745076 original size:52 final size:54
Alignment explanation
Indices: 20744963--20745077 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 54
20744953 ACATCTTTTC
* *
20744963 AAAAATTTTCGTGTTTCAAAAATTTCTCGTGTTTTCAAAAAAATTCTTGTGTTT
1 AAAAATTTTCGTATTTCAAAAATTTCTCATGTTTTCAAAAAAATTCTTGTGTTT
*
20745017 AAAAATTTTCGTATTTCAAAACTTT-TCATGTTTTC-AAAAAATTCTTGTGTTT
1 AAAAATTTTCGTATTTCAAAAATTTCTCATGTTTTCAAAAAAATTCTTGTGTTT
20745069 AAAAATTTT
1 AAAAATTTT
20745078 TCGCGTTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 26 0.45
53 9 0.16
54 23 0.40
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (54 bp):
AAAAATTTTCGTATTTCAAAAATTTCTCATGTTTTCAAAAAAATTCTTGTGTTT
Found at i:20745104 original size:37 final size:36
Alignment explanation
Indices: 20744959--20745244 Score: 172
Period size: 37 Copynumber: 7.8 Consensus size: 36
20744949 CGATACATCT
* *
20744959 TTTCAAAAATTTTCGTG-TTTC-AAAAATTTCTCGTG
1 TTTCAAAAATTTTCGCGTTTTCAAAAAATTT-TTGTG
** ** * *
20744994 TTTTCAAAAAAATTCTTGTGTTT--AAAAATTTTCGTA
1 -TTTCAAAAATTTTCGCGT-TTTCAAAAAATTTTTGTG
* ** *
20745030 TTTCAAAACTTTTCATGTTTTCAAAAAATTCTTGTG
1 TTTCAAAAATTTTCGCGTTTTCAAAAAATTTTTGTG
20745066 TTT-AAAAATTTTTCGCGTTTTCAAAAAATTTTTGGTG
1 TTTCAAAAA-TTTTCGCGTTTTCAAAAAATTTTT-GTG
* **
20745103 TTTCAAAAATTTTCGCATTTTCAAAATTTTTTTCGTG
1 TTTCAAAAATTTTCGCGTTTTCAAAAAATTTTT-GTG
* * *
20745140 TTTCAAAGAA-TTTCGTGTTTTCAAAAAAAAAAAGTTCT-TG
1 TTTCAAA-AATTTTCGCGTTTTC-----AAAAAATTTTTGTG
* * * *
20745180 TTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTG
1 TTTCAAAAATTTTCGCGTTTTCAAAAAATTTTTGTG
** *
20745216 TTTCCAAAAAAATTCTCGTGTTTCAAAAA
1 TTT-CAAAAATTTTCGCGT-TTTCAAAAA
20745245 TTTCCGTGTT
Statistics
Matches: 200, Mismatches: 33, Indels: 32
0.75 0.12 0.12
Matches are distributed among these distances:
34 3 0.01
35 27 0.14
36 57 0.28
37 65 0.32
38 19 0.09
39 1 0.00
40 21 0.10
42 7 0.04
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (36 bp):
TTTCAAAAATTTTCGCGTTTTCAAAAAATTTTTGTG
Found at i:20745283 original size:56 final size:54
Alignment explanation
Indices: 20745178--20745299 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 54
20745168 AAAAAGTTCT
* *
20745178 TGTTTCAAAAGTTTTCGTGTTTTCAAAAAAGTTTAGTGTTTCCAAAAAAATTCTCG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAGTTTAGTGTTTCC-AAAAAA-TCTCG
* *
20745234 TGTTTCAAAAATTTCCGTGTTTTCAGAAAATTATTATGGTGTTT-C-AAAAATCTCG
1 TGTTTCAAAAATTTCCGTGTTTTCAAAAAAGT-TTA--GTGTTTCCAAAAAATCTCG
*
20745289 TGTTTTAAAAA
1 TGTTTCAAAAA
20745300 AAATATCATG
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
55 15 0.26
56 33 0.57
57 3 0.05
58 1 0.02
59 6 0.10
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (54 bp):
TGTTTCAAAAATTTCCGTGTTTTCAAAAAAGTTTAGTGTTTCCAAAAAATCTCG
Found at i:20747544 original size:24 final size:23
Alignment explanation
Indices: 20747517--20747564 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
20747507 TAGTTTTAAG
20747517 ATTTATCCTTTTATAAAAAATTTC
1 ATTTAT-CTTTTATAAAAAATTTC
* *
20747541 ATTTATTTTTTATAAATAATTTC
1 ATTTATCTTTTATAAAAAATTTC
20747564 A
1 A
20747565 AAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTATCTTTTATAAAAAATTTC
Found at i:20748358 original size:14 final size:14
Alignment explanation
Indices: 20748339--20748377 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20748329 TTGTTTCACT
*
20748339 GAAAATGACTTCTG
1 GAAAATGACTTCTA
*
20748353 GAAAATGATTTCTA
1 GAAAATGACTTCTA
20748367 GAAAATGACTT
1 GAAAATGACTT
20748378 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (14 bp):
GAAAATGACTTCTA
Found at i:20749465 original size:27 final size:27
Alignment explanation
Indices: 20749431--20749494 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
20749421 ATAAAAAATA
*
20749431 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
20749458 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
20749485 ACCAAAATAT
1 ACCAAAATAT
20749495 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:20749574 original size:27 final size:27
Alignment explanation
Indices: 20749544--20749620 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
20749534 GGCCAATCAC
*
20749544 ATTGGCGGCACCAAAGGTGCCAATGTA
1 ATTGGCGGCACCAATGGTGCCAATGTA
* *
20749571 ATTGGCAGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTA
20749598 ATTGGCGGCACCAATGGTGCCAA
1 ATTGGCGGCACCAATGGTGCCAA
20749621 AGGACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATGTA
Found at i:20751091 original size:10 final size:10
Alignment explanation
Indices: 20751065--20751097 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20751055 TATAAGAATT
20751065 ATAAATAAAA
1 ATAAATAAAA
*
20751075 AT-TATAAAA
1 ATAAATAAAA
20751084 ATAAATAAAA
1 ATAAATAAAA
20751094 ATAA
1 ATAA
20751098 CTATATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:20753190 original size:21 final size:20
Alignment explanation
Indices: 20753149--20753191 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
20753139 AGAAAATAAA
* *
20753149 TAAAATCATTTGTAGTTCTT
1 TAAAATCATTTGTAATACTT
20753169 TAAAATCATGTTGTAATACTT
1 TAAAATCAT-TTGTAATACTT
20753190 TA
1 TA
20753192 TAATTGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (20 bp):
TAAAATCATTTGTAATACTT
Found at i:20754610 original size:6 final size:6
Alignment explanation
Indices: 20754599--20754695 Score: 68
Period size: 6 Copynumber: 16.2 Consensus size: 6
20754589 TATCTAAGTA
* * * * *
20754599 ACACAC ACACAC ACACAC ACACAC ACACAA AGACCC ACACCC ACACCC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* * * * * * * * *
20754647 ACACCC ACACCC TCACCC ACACCC ACACCC ACATAC ACATAT ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
20754695 A
1 A
20754696 TATATATCAT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.42, C:0.53, G:0.01, T:0.04
Consensus pattern (6 bp):
ACACAC
Found at i:20754622 original size:18 final size:18
Alignment explanation
Indices: 20754599--20754685 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 18
20754589 TATCTAAGTA
*
20754599 ACACACACACACACACAC
1 ACACACACACACACACCC
* *
20754617 ACACACACACAAAGACCC
1 ACACACACACACACACCC
* *
20754635 ACACCCACACCCACACCC
1 ACACACACACACACACCC
* * *
20754653 ACACCCTCACCCACACCC
1 ACACACACACACACACCC
* *
20754671 ACACCCACATACACA
1 ACACACACACACACA
20754686 TATACACACA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.41, C:0.55, G:0.01, T:0.02
Consensus pattern (18 bp):
ACACACACACACACACCC
Found at i:20759813 original size:22 final size:22
Alignment explanation
Indices: 20759786--20759827 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20759776 TAAGAATTGT
20759786 ATTAAATTGAGTGAAATTTAGA
1 ATTAAATTGAGTGAAATTTAGA
*
20759808 ATTAAATTGAGTTAAATTTA
1 ATTAAATTGAGTGAAATTTA
20759828 CTTATATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTAAATTGAGTGAAATTTAGA
Found at i:20773183 original size:17 final size:17
Alignment explanation
Indices: 20773161--20773196 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20773151 AACCTTATTC
*
20773161 AAAGGTTGAAAAACCTT
1 AAAGGTTGAAAAAACTT
20773178 AAAGGTTGAAAAAACTT
1 AAAGGTTGAAAAAACTT
20773195 AA
1 AA
20773197 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (17 bp):
AAAGGTTGAAAAAACTT
Found at i:20774246 original size:94 final size:94
Alignment explanation
Indices: 20774080--20774333 Score: 276
Period size: 94 Copynumber: 2.7 Consensus size: 94
20774070 TGCTCAACTG
* * * * * *
20774080 CAACCTCAGGGGCATAAGAATTGTACCTTC-ATCTTGCTCCACTGCAACTTAAGGGAGATAAGAT
1 CAACTTCAGGGGTAAAAGATTTGTAGCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
20774144 TCACTATGGTAGATTCAATCAAACCTATTA
65 TTACTATGGTAGATTCAATCAAACCCACTA
* *
20774174 CAACTTCAGGGGTAAAAGTTTTGTAGCTTCAATCTGCTTCACTGCAACTTCAGGGAGATAAGATT
1 CAACTTCAGGGGTAAAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
* ** *
20774239 TTCTATGGTAGATTCAATCTGACCCACTG
66 TACTATGGTAGATTCAATCAAACCCACTA
* ** * * * * * *
20774268 TAACTTCAGGGGTGTAGGATTTGTAGCTTTAATTTGCTCCACTGTAACTCCAAGGAGATAAGATT
1 CAACTTCAGGGGTAAAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
20774333 T
66 T
20774334 GTAGCTTCAT
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
94 130 0.98
95 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (94 bp):
CAACTTCAGGGGTAAAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
TACTATGGTAGATTCAATCAAACCCACTA
Found at i:20774276 original size:50 final size:50
Alignment explanation
Indices: 20774118--20774278 Score: 147
Period size: 50 Copynumber: 3.3 Consensus size: 50
20774108 TCATCTTGCT
* ** **
20774118 CCACTGCAACTTAAGGGAGATAAGATTCACTATGGTAGATTCAATCAAAC
1 CCACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAATCTGAC
* * * ** *
20774168 CTATTACAACTTCAGGG-G-TAA-AAGTT-T-T-GTAGCTTCAATCTG-C
1 CCACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAATCTGAC
*
20774211 TTCACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAATCTGAC
1 -CCACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAATCTGAC
*
20774262 CCACTGTAACTTCAGGG
1 CCACTGCAACTTCAGGG
20774279 GTGTAGGATT
Statistics
Matches: 83, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
43 1 0.01
44 24 0.29
45 2 0.02
46 4 0.05
47 4 0.05
48 4 0.05
49 2 0.02
50 41 0.49
51 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (50 bp):
CCACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAATCTGAC
Found at i:20774369 original size:44 final size:45
Alignment explanation
Indices: 20773988--20774512 Score: 226
Period size: 44 Copynumber: 11.6 Consensus size: 45
20773978 ATTCCAACCT
* * ** *
20773988 ACTGCAACTTCAGGG-GTATAGGAATTGTATTTTCAATC-TGATCC
1 ACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTTGCTCC
** * * * * *
20774032 ACTAAAACTTTAGGGATATAGGAGTTGTAGCTTC-ATCTTGCTCA
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTTGCTCC
* * *
20774076 ACTGCAACCTCAGGG-GCATAAGAATTGTACCTTC-ATCTTGCTCC
1 ACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTTGCTCC
* * *** *
20774120 ACTGCAACTTAAGGGAGATAAGATTCACTATGGTAGATTCAATCAAAC-CT
1 ACTGCAACTTCAGGGAGATAAGA-T---T-T-GTAGCTTCAATCTTGCTCC
* * * * *
20774170 ATTACAACTTCAGGG-GTAAAAGTTTTGTAGCTTCAATC-TGCTTC
1 ACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTTGCTCC
*
20774214 ACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAATC-TGAC-CC
1 ACTGCAACTTCAGGGAGATAAGA---T-T-T-GTAGCTTCAATCTTG-CTCC
* * * *
20774264 ACTGTAACTTCAGGG-GTGTAGGATTTGTAGCTTTAAT-TTGCTCC
1 ACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTTGCTCC
* * *
20774308 ACTGTAACTCCAAGGAGATAAGATTTGTAGCTTC-ATCTTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTTGCTCC
* * ***
20774352 ACTGCAACTTCAGGGAGATAAGATCCACCATTGTAGTTTCATTCCAAC-CC
1 ACTGCAACTTCAGGGAGATAAGAT------TTGTAGCTTCAATCTTGCTCC
** * * * * *
20774402 ACAACAACTTTAGGG-G-TATAGAAATTGTAGCGTCAATC-TGATGC
1 ACTGCAACTTCAGGGAGATA-AG-ATTTGTAGCTTCAATCTTGCTCC
* * * *
20774446 ACTACAACTTCA-AG-GATAGGATTTGTAGTTTC-ATCTTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTTGCTCC
*
20774488 ACTGCAACTTCAAGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
20774513 CACTATGGTA
Statistics
Matches: 357, Mismatches: 84, Indels: 80
0.69 0.16 0.15
Matches are distributed among these distances:
41 3 0.01
42 24 0.07
43 11 0.03
44 211 0.59
45 5 0.01
46 2 0.01
47 2 0.01
48 4 0.01
49 8 0.02
50 79 0.22
51 8 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (45 bp):
ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTTGCTCC
Found at i:20774432 original size:232 final size:231
Alignment explanation
Indices: 20774019--20774457 Score: 535
Period size: 232 Copynumber: 1.9 Consensus size: 231
20774009 GAATTGTATT
* * *
20774019 TTCAATCTGATCCACTAAAACTTTAGGGATATAGGAGTTGTAGCTTCATCTTGCTCAACTGCAAC
1 TTCAATCTGACCCACTAAAACTTCAGGGATATAGGAGTTGTAGCTTAATCTTGCTCAACTGCAAC
* * *
20774084 CTCAGGGGCATAAGAATTGTACCTTCATCTTGCTCCACTGCAACTTAAGGGAGATAAGATTCACT
66 CTCAGGAGCATAAGAATTGTACCTTCATCTTGCTCCACTGCAACTTAAGGGAGATAAGATCCACC
* ** * * * *
20774149 ATGGTAGATTCAATCAAACCTATTACAACTTCAGGGGTAAAAGTTTTGTAGCTTCAATCTGCTTC
131 ATGGTAGATTCAATCAAACCCACAACAACTTCAGGGGTAAAAG-ATTGTAGCGTCAATCTGATGC
*
20774214 ACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGA
195 ACTACAACTTCAGGGAGATAAGATTTTCTATGGTAGA
** * * * * *
20774251 TTCAATCTGACCCACTGTAACTTCAGGGGTGTAGGATTTGTAGCTTTAAT-TTGCTCCACTGTAA
1 TTCAATCTGACCCACTAAAACTTCAGGGATATAGGAGTTGTAGC-TTAATCTTGCTCAACTGCAA
* * *
20774315 -CTCCAAGGAG-ATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATCC
65 CCT-C-AGGAGCATAAGAATTGTACCTTCATCTTGCTCCACTGCAACTTAAGGGAGATAAGATCC
* * * * *
20774378 ACCATTGTAGTTTCATTCCAACCCACAACAACTTTAGGGGTATAGAA-ATTGTAGCGTCAATCTG
128 ACCATGGTAGATTCAATCAAACCCACAACAACTTCAGGGGTA-A-AAGATTGTAGCGTCAATCTG
20774442 ATGCACTACAACTTCA
191 ATGCACTACAACTTCA
20774458 AGGATAGGAT
Statistics
Matches: 173, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
231 2 0.01
232 160 0.92
233 9 0.05
234 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (231 bp):
TTCAATCTGACCCACTAAAACTTCAGGGATATAGGAGTTGTAGCTTAATCTTGCTCAACTGCAAC
CTCAGGAGCATAAGAATTGTACCTTCATCTTGCTCCACTGCAACTTAAGGGAGATAAGATCCACC
ATGGTAGATTCAATCAAACCCACAACAACTTCAGGGGTAAAAGATTGTAGCGTCAATCTGATGCA
CTACAACTTCAGGGAGATAAGATTTTCTATGGTAGA
Found at i:20774547 original size:136 final size:138
Alignment explanation
Indices: 20774193--20774574 Score: 448
Period size: 136 Copynumber: 2.8 Consensus size: 138
20774183 GGGTAAAAGT
* **
20774193 TTTGTAGCTTCAATC-TGCTTCACTGCAACTTCAGGGAGATAAGATTTTCTATGGTAGATTCAAT
1 TTTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTATGGTAGATTCAAT
* * * * * * * * **
20774257 CTGACCCACTGTAACTTCAGGGGTGTAGGATTTGTAGCTTTAATTTGCTCCACTGTAACTCCAAG
65 CCGACCCACTGTAACTTCAGGGGTATAGAAATTGTAGCATCAATCTGATCCACTACAACTCCAAG
20774322 GAGATAAGA
130 GAGATAAGA
* * * * *
20774331 TTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATCCACCATTGTAGTTTCATTC
1 TTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTATGGTAGATTCAATC
* *** * * * *
20774396 CAACCCACAACAACTTTAGGGGTATAGAAATTGTAGCGTCAATCTGATGCACTACAACTTCAA-G
66 CGACCCACTGTAACTTCAGGGGTATAGAAATTGTAGCATCAATCTGATCCACTACAACTCCAAGG
*
20774460 -GATAGGA
131 AGATAAGA
* *
20774467 TTTGTAGTTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCACTATGGTA-AGTTCAAT
1 TTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTATGGTAGA-TTCAAT
*
20774531 CCGAGCCACTGTAACTTCAGGGGTATAGAAATTGTAGCATCAAT
65 CCGACCCACTGTAACTTCAGGGGTATAGAAATTGTAGCATCAAT
20774575 TAGGGGTGCG
Statistics
Matches: 202, Mismatches: 40, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
136 99 0.49
137 4 0.02
138 99 0.49
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (138 bp):
TTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCACTATGGTAGATTCAATC
CGACCCACTGTAACTTCAGGGGTATAGAAATTGTAGCATCAATCTGATCCACTACAACTCCAAGG
AGATAAGA
Found at i:20779086 original size:17 final size:17
Alignment explanation
Indices: 20779066--20779126 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
20779056 ATTTCAAGAC
20779066 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ** *
20779083 TTATGTAGTGATTCAAATAC
1 TTATGTAATG-TT--TTTAA
20779103 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
20779120 TTATGTA
1 TTATGTA
20779127 GTGATTCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 2 0.06
20 11 0.33
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.52
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:20779105 original size:37 final size:37
Alignment explanation
Indices: 20779064--20779135 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
20779054 TAATTTCAAG
20779064 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAT
1 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAT
20779101 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAA
1 ACTTATGTAATGTTTTTAATTATGTAGTGATTCAA
20779136 TTCGGGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.49
Consensus pattern (37 bp):
ACTTATGTAATGTTTTTAATTATGTAGTGATTCAAAT
Found at i:20789804 original size:2 final size:2
Alignment explanation
Indices: 20789797--20789826 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20789787 CTGTTTATTC
*
20789797 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20789827 TCTTGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:20790076 original size:23 final size:23
Alignment explanation
Indices: 20790037--20790084 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20790027 TTTTAAATGA
20790037 TTTTATAAATAATTTATTTAATT
1 TTTTATAAATAATTTATTTAATT
* *
20790060 TTTTATATAT-ATATTATTTTATT
1 TTTTATAAATAAT-TTATTTAATT
20790083 TT
1 TT
20790085 GAATTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATAAATAATTTATTTAATT
Found at i:20793992 original size:14 final size:12
Alignment explanation
Indices: 20793959--20794001 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
20793949 AAAGTGCCAA
20793959 AAATAATAAAAG
1 AAATAATAAAAG
20793971 AAATAATAAAATG
1 AAATAATAAAA-G
*
20793984 ATGATAATAAAA-
1 A-AATAATAAAAG
20793996 AAATAA
1 AAATAA
20794002 GATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.15
12 12 0.44
13 2 0.07
14 9 0.33
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
AAATAATAAAAG
Found at i:20794741 original size:29 final size:28
Alignment explanation
Indices: 20794678--20794740 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
20794668 TTAAGTTAAA
*
20794678 TTTTTTTGAAAAAAATCCATTTCATCCC
1 TTTTTTTAAAAAAAATCCATTTCATCCC
* * *
20794706 TTGTTTTAAAAAAAACTTCATTTC-TCCT
1 TTTTTTTAAAAAAAA-TCCATTTCATCCC
20794734 TTTTTTT
1 TTTTTTT
20794741 TCTCTCAGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (28 bp):
TTTTTTTAAAAAAAATCCATTTCATCCC
Found at i:20797488 original size:3 final size:3
Alignment explanation
Indices: 20797482--20797526 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20797472 CATCATCATC
20797482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20797527 GAATGTATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20803993 original size:17 final size:18
Alignment explanation
Indices: 20803971--20804005 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20803961 ACAACTTCTA
20803971 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
20803988 TTAAATGTATAGTTATTT
1 TTAAATGTATAATTATTT
20804006 CAACTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Found at i:20804012 original size:44 final size:44
Alignment explanation
Indices: 20803936--20804060 Score: 198
Period size: 44 Copynumber: 2.9 Consensus size: 44
20803926 ATTCTTATTC
* * **
20803936 TAATTATTTTT-AATGTGTAATTATCACAACTTCTATTAAATTA
1 TAATTATTTTTAAATGTATAGTTATTTCAACTTCTATTAAATTA
20803979 TAATTATTTTTAAATGTATAGTTATTTCAACTTCTATTAAATTA
1 TAATTATTTTTAAATGTATAGTTATTTCAACTTCTATTAAATTA
*
20804023 TAATTATTTTTAAATGTATAGTTATTTCACCTTCTATT
1 TAATTATTTTTAAATGTATAGTTATTTCAACTTCTATT
20804061 TTGTTTAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
43 11 0.14
44 65 0.86
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (44 bp):
TAATTATTTTTAAATGTATAGTTATTTCAACTTCTATTAAATTA
Found at i:20804037 original size:17 final size:18
Alignment explanation
Indices: 20804015--20804049 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20804005 TCAACTTCTA
20804015 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
20804032 TTAAATGTATAGTTATTT
1 TTAAATGTATAATTATTT
20804050 CACCTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Done.