Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007053.1 Hibiscus syriacus cultivar Beakdansim tig00018289_pilon, 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: 65936
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:181 original size:19 final size:20
Alignment explanation
Indices: 145--188 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
135 ATATGAATTT
145 TCAAAACAACATAATT-AAA
1 TCAAAACAACATAATTAAAA
*
164 TCAAAACAACA-ATTTTAAAA
1 TCAAAACAACATA-ATTAAAA
184 TCAAA
1 TCAAA
189 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (20 bp):
TCAAAACAACATAATTAAAA
Found at i:6512 original size:65 final size:65
Alignment explanation
Indices: 6440--6587 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 65
6430 TACACTAGGG
* * *
6440 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCT-AGGAGTGCATCGATGCATGG
1 GTGCATCGGTACACTAAAATACATTCAATGTTTCAATAA-A-CTAAAGAGTGCATCGATGCATGG
*
6502 TCT
64 -AT
* * *
6505 GTGCATCGGTACA-TAAAATGCATTCAATGTTTCAATAAATTAAAGAGTGCATCGATGTATGGAT
1 GTGCATCGGTACACTAAAATACATTCAATGTTTCAATAAACTAAAGAGTGCATCGATGCATGGAT
6569 GTGCATCGGTACAC-AAAAT
1 GTGCATCGGTACACTAAAAT
6588 GCTTTCAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
64 21 0.29
65 49 0.68
66 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAAATACATTCAATGTTTCAATAAACTAAAGAGTGCATCGATGCATGGAT
Found at i:15619 original size:12 final size:12
Alignment explanation
Indices: 15597--15628 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
15587 TCAAGAGATA
15597 AAAAGAAAATAAG
1 AAAA-AAAATAAG
15610 AAAAAAAATAAG
1 AAAAAAAATAAG
15622 AAAAAAA
1 AAAAAAA
15629 CAAATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAAAAAATAAG
Found at i:15659 original size:16 final size:16
Alignment explanation
Indices: 15638--15668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15628 ACAAATAGAA
*
15638 ATGGTATATATATAAT
1 ATGGTATATAAATAAT
15654 ATGGTATATAAATAA
1 ATGGTATATAAATAA
15669 AAAATATAAA
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:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
ATGGTATATAAATAAT
Found at i:15693 original size:11 final size:12
Alignment explanation
Indices: 15659--15697 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
15649 ATAATATGGT
*
15659 ATATAAATAAAAA
1 ATATAAAT-AATA
15672 ATATAAATAATA
1 ATATAAATAATA
15684 ATAT-AATAATA
1 ATATAAATAATA
15695 ATA
1 ATA
15698 CACATATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 7 0.28
13 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:16907 original size:2 final size:2
Alignment explanation
Indices: 16900--16926 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16890 CATGTAAATA
16900 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 A
16927 ACATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17594 original size:36 final size:36
Alignment explanation
Indices: 17464--17597 Score: 184
Period size: 36 Copynumber: 3.7 Consensus size: 36
17454 CGAAGGTTTG
*
17464 GTGTTTTAAGAGAAACAATTTCAAAGGTTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTTT
17501 GTGTTTCAAGAG-AA-AATGTCTC-AAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAAT-T-TCAAAGGTTTTTTTTT
* **
17536 GTGTTTCAAGAAAAACTGTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
17572 GTGTTTCAAGAGAAACAATTTCAAAG
1 GTGTTTCAAGAGAAACAATTTCAAAG
17598 ATTGGTGCTT
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
35 25 0.29
36 46 0.54
37 14 0.16
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:17691 original size:36 final size:36
Alignment explanation
Indices: 17606--18304 Score: 592
Period size: 36 Copynumber: 19.9 Consensus size: 36
17596 AGATTGGTGC
* *
17606 TTCAATAGAAACTGTCTCAAGAGAGGCAAAACTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* *
17643 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
17679 TTCAAGATAAACTGTCTCAAGAGAGACAAAACTTAGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* *
17716 TCCAAAAGAAACTGTCTCAAGAGAGACGAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGT
* * *
17753 TTAAAG-GAAAACAGAT-TC-----A-A-AAATTTTGT
1 TTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATTTGT
*
17782 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
17818 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATCTAGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-TTGT
* * * * *
17855 TCCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
17891 TTCAAG-GAAAACAGAT-TC-A-A-AG----ATTTTAT
1 TTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATTTGT
* * * *
17920 TTCAAGGGAAACTGTTTCAAGAGAGATAAAACTTAGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* * * *
17957 TCCAAAAGAAATTGTCTCGAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
17993 TTAAAG-GAAAACAGAT-T-TA-A-AG----ATTTTGT
1 TTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATTTGT
* * *
18022 TTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
18058 TCCAATGA-AAACTGTCTCAATAGAGACAAAATTTGT
1 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
18094 TTTAAGAGAAAATGTCTCAAGAGAGAAAAAAATTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
*
18130 TTTACA-AGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCA-AGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
18166 TTTAAGAGAAAATGTCTCAAAAGAGACAAAATTTAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
18202 TTTACGAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
18238 TTTACGAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
18274 TTTAAGAGAAACCGTCTCAAGAGAGACAAAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA
18305 CTTTATTTTG
Statistics
Matches: 539, Mismatches: 82, Indels: 83
0.77 0.12 0.12
Matches are distributed among these distances:
28 3 0.01
29 55 0.10
30 5 0.01
31 3 0.01
32 5 0.01
33 4 0.01
34 2 0.00
35 8 0.01
36 320 0.59
37 129 0.24
38 5 0.01
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:17799 original size:139 final size:138
Alignment explanation
Indices: 17633--17988 Score: 534
Period size: 139 Copynumber: 2.6 Consensus size: 138
17623 CAAGAGAGGC
* *
17633 AAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGATAAACTGTCTCA
1 AAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCA
17698 AGAGAGACAAAA-CTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAAATTTGTTTAAAGGAA
66 AGAGAGACAAAATC-TAGTTCCAAAAGAAACTGTCTCAAGAGAGACG-AAATTTGTTTAAAGGAA
17762 AACAGATTCA
129 AACAGATTCA
* *
17772 AAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCA
1 AAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCA
* * *
17837 AGAGAGACAAAATCTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAA
66 AGAGAGACAAAATCTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAA
17902 CAGATTCA
131 CAGATTCA
* * * * * * * *
17910 AAGATTTTATTTCAAGGGAAACTGTTTCAAGAGAGATAAAACTTAGTTCCAAAAGAAATTGTCTC
1 AAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGAGAAACTGTCTC
*
17975 GAGAGAGACAAAAT
65 AAGAGAGACAAAAT
17989 TTGTTTAAAG
Statistics
Matches: 197, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
138 65 0.33
139 131 0.66
140 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (138 bp):
AAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCA
AGAGAGACAAAATCTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAA
CAGATTCA
Found at i:17923 original size:102 final size:102
Alignment explanation
Indices: 17817--18105 Score: 395
Period size: 102 Copynumber: 2.8 Consensus size: 102
17807 ACAAAATTTG
*
17817 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATCTAGTTCCAAAAGAAATTGTCTCAAGGGAGAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATCTAGTTCCAAAAGAAATTGTCTCAAGAGAGAC
* *
17882 GAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTA
66 AAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTA
* * *
17919 TTTCAAGGGAAACTGTTTCAAGAGAGATAAAA-CTTAGTTCCAAAAGAAATTGTCTCGAGAGAGA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATC-TAGTTCCAAAAGAAATTGTCTCAAGAGAGA
* *
17983 CAAAATTTGTTTAAAGGAAAACAGATTTAAAGATTTTG
65 CAAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTA
* * * * * *
18021 TTTTAAGGGAAACTGTCTCAAGAGAGACAAAAT-TTGATCC-AATGAAAACTGTCTCAATAGAGA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATCTAGTTCCAAAAG-AAATTGTCTCAAGAGAGA
*
18084 CAAAATTTGTTTTAAGAGAAAA
65 CAAAATTTGTTTAAAG-GAAAA
18106 TGTCTCAAGA
Statistics
Matches: 165, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
100 3 0.02
101 36 0.22
102 126 0.76
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (102 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATCTAGTTCCAAAAGAAATTGTCTCAAGAGAGAC
AAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTA
Found at i:19737 original size:95 final size:95
Alignment explanation
Indices: 19569--19750 Score: 303
Period size: 95 Copynumber: 1.9 Consensus size: 95
19559 ATATGTAAAT
* *
19569 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
*
19634 ACAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
* *
19664 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCT-TAGAGG
19728 GACAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
19751 TAAATAATAT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 2 0.02
95 79 0.98
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:23568 original size:8 final size:8
Alignment explanation
Indices: 23524--23587 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 8
23514 ACTTAAGGAA
23524 AAAATAAAT
1 AAAA-AAAT
23533 AAATAAAAT
1 AAA-AAAAT
* * *
23542 CAAGAGAT
1 AAAAAAAT
*
23550 AAAAAGA-
1 AAAAAAAT
23557 AAAAAAAT
1 AAAAAAAT
23565 AAAAAAAT
1 AAAAAAAT
23573 -AAAAAAT
1 AAAAAAAT
23580 AAGAAAAA
1 AA-AAAAA
23588 AACAAATACA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 13 0.29
8 17 0.38
9 14 0.31
10 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:23654 original size:11 final size:12
Alignment explanation
Indices: 23620--23658 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
23610 ATATTATGGT
*
23620 ATATAAATAAAAA
1 ATATAAAT-AATA
23633 ATATAAATAATA
1 ATATAAATAATA
23645 ATAT-AATAATA
1 ATATAAATAATA
23656 ATA
1 ATA
23659 ATTCACGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 7 0.28
13 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:23825 original size:17 final size:18
Alignment explanation
Indices: 23803--23843 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23793 GAAAAGTAAA
23803 ACTAAAAT-TAAAAAAGG
1 ACTAAAATCTAAAAAAGG
23820 ACT-AAATCGTAAAAAAGG
1 ACTAAAATC-TAAAAAAGG
23838 A-TAAAA
1 ACTAAAA
23844 CAAGTGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.17
Consensus pattern (18 bp):
ACTAAAATCTAAAAAAGG
Found at i:24892 original size:2 final size:2
Alignment explanation
Indices: 24885--24937 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
24875 CATGTAAATA
24885 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
24927 AT AT AT AT AT A
1 AT AT AT AT AT A
24938 ACATATAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26756 original size:13 final size:14
Alignment explanation
Indices: 26740--26768 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
26730 ATGTTCTTAT
26740 ATTTT-TATAAGAA
1 ATTTTCTATAAGAA
26753 ATTTTCTATAAGAA
1 ATTTTCTATAAGAA
26767 AT
1 AT
26769 GTATTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (14 bp):
ATTTTCTATAAGAA
Found at i:29500 original size:76 final size:77
Alignment explanation
Indices: 29380--29570 Score: 226
Period size: 76 Copynumber: 2.5 Consensus size: 77
29370 ATAGTTTGTG
* *** * ** *
29380 ATCTGAAATATTAATATTTTTATTAATAAAATAGGTTATGCCCAAGAATATCATGGTTGACTTAA
1 ATCTGAAATGTTAATATTTTTATTAATAAAATAGGTTGCACCCAAGAATATAATAATTCAC-TAA
*
29445 -AAATAGGTTACT-
65 GAAATAAGTT-CTA
* *
29457 ATTTGGAATGTTAATATTTTT-TTAATAAAATAGGTTGCACCCAAGAATATAATAATTCACTAAG
1 ATCTGAAATGTTAATATTTTTATTAATAAAATAGGTTGCACCCAAGAATATAATAATTCACTAAG
*
29521 AAATAAGTTTTA
66 AAATAAGTTCTA
*
29533 ATCTGAAATGTTAATATTTTTATTAATAAAATGGGTTG
1 ATCTGAAATGTTAATATTTTTATTAATAAAATAGGTTG
29571 AGCCTAAAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
75 4 0.04
76 59 0.61
77 33 0.34
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (77 bp):
ATCTGAAATGTTAATATTTTTATTAATAAAATAGGTTGCACCCAAGAATATAATAATTCACTAAG
AAATAAGTTCTA
Found at i:31446 original size:23 final size:24
Alignment explanation
Indices: 31415--31467 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
31405 TTCATTTAAC
* *
31415 GTTCGTTTA-ATATTCGCGAACAT
1 GTTCATTTATATATTCACGAACAT
* *
31438 GTTCATTTATATGTTCACGAACGT
1 GTTCATTTATATATTCACGAACAT
31462 GTTCAT
1 GTTCAT
31468 GAACACGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (24 bp):
GTTCATTTATATATTCACGAACAT
Found at i:32354 original size:60 final size:60
Alignment explanation
Indices: 32290--32405 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
32280 TATGTCATTT
* *
32290 ATTATA-GAATATTATTTTGTTAAGTACTT-TAATTATTAAAAGTTATAAAATAATCTCTAA
1 ATTATATG-ATATTATTTTGTTAAGT-CTTCTAATTATTAAAACTTACAAAATAATCTCTAA
* * * * *
32350 ATTATATGTTATTGTTTTGTTGAGTCTTCTAATTTTTAAAACTTACAAAATTATCT
1 ATTATATGATATTATTTTGTTAAGTCTTCTAATTATTAAAACTTACAAAATAATCT
32406 TTCAACAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.06
60 43 0.91
61 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (60 bp):
ATTATATGATATTATTTTGTTAAGTCTTCTAATTATTAAAACTTACAAAATAATCTCTAA
Found at i:32678 original size:43 final size:43
Alignment explanation
Indices: 32622--32706 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
32612 TTCAAAAGAA
*
32622 TACAACTACTCTTCTTCCAAACCTTTAAACCCT-TCGAAAAAAG
1 TACAACCACTCTTCTTCCAAACCTTTAAACCCTAT-GAAAAAAG
* *
32665 TACAACCACTCTTCTTCCAAACTTTTAAATCCTATGAAAAAA
1 TACAACCACTCTTCTTCCAAACCTTTAAACCCTATGAAAAAA
32707 AAATACACAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.29
Consensus pattern (43 bp):
TACAACCACTCTTCTTCCAAACCTTTAAACCCTATGAAAAAAG
Found at i:39751 original size:28 final size:28
Alignment explanation
Indices: 39711--39767 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39701 TCGAAAAAGT
39711 TGGTTTACTGACGGTTAGCTTCAGTATC
1 TGGTTTACTGACGGTTAGCTTCAGTATC
39739 TGGTTTACTGACGGTTAGCTTCAGTATC
1 TGGTTTACTGACGGTTAGCTTCAGTATC
39767 T
1 T
39768 CCAATATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (28 bp):
TGGTTTACTGACGGTTAGCTTCAGTATC
Found at i:41138 original size:26 final size:26
Alignment explanation
Indices: 41074--41139 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
41064 TATCACACTA
*
41074 TAAAAAAGAATTAGTATAAATAAAAATT
1 TAAAAAA-AATAAG-ATAAATAAAAATT
**
41102 TAAAATTAATAAGATAAATAAAAA-T
1 TAAAAAAAATAAGATAAATAAAAATT
41127 TAAACAAAAATAA
1 TAAA-AAAAATAA
41140 TACATCTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 5 0.16
26 17 0.53
27 5 0.16
28 5 0.16
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (26 bp):
TAAAAAAAATAAGATAAATAAAAATT
Found at i:42642 original size:142 final size:141
Alignment explanation
Indices: 42375--42746 Score: 424
Period size: 142 Copynumber: 2.6 Consensus size: 141
42365 TTGTTTTAAA
* * * *
42375 AAAAACGTATAATATATAGTTTTTAAAATAATTTTAAAAGCGTATAAATATATAGTTTTTCAAAA
1 AAAAACATATAATATATAGTTTTTAAAATAGTTTGAAAA-CGTAT-AATATATAGTTTTTAAAAA
* * * **
42440 TAGTTTGGAAAGCGTATAATATATAGTTTTTAAAAATAGTTTTGAAAATGTATAATATATAATTT
64 TAGTTTTGAAAACGTATAATATATAGTTTTTAAAAACAGTTTTGAAAACATATAATATATAATTT
*
42505 TTAAAACGGGTTT
129 TCAAAACGGGTTT
* ** *
42518 GAAAACATATGGTATATAGTTTTTAAAATAGTTTGGAAAATGTATAATATATAGTTTTTAAAAAT
1 AAAAACATATAATATATAGTTTTTAAAATAGTTT-GAAAACGTATAATATATAGTTTTTAAAAAT
*
42583 AGTTTTGAAAACGTATAATATATAGTTTTTAAAAACAGTTTTGAAAACATAT-ATAATATAGTTT
65 AGTTTTGAAAACGTATAATATATAGTTTTTAAAAACAGTTTTGAAAACATATAAT-ATATAATTT
* * *
42647 TCGAAATGGTTTT
129 TCAAAACGGGTTT
* * * ** * *
42660 AAAAACGTATAATATACATTTTTTTAAAGGATTTTGAAAACGTATAATATATA-TTTTAAAAAAC
1 AAAAACATATAATATATA-GTTTTTAAAATAGTTTGAAAACGTATAATATATAGTTTTTAAAAA-
** *
42724 TTTTTTTGAAAACATATAATATA
64 TAGTTTTGAAAACGTATAATATA
42747 ATACTATATA
Statistics
Matches: 193, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
141 11 0.06
142 133 0.69
143 45 0.23
144 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (141 bp):
AAAAACATATAATATATAGTTTTTAAAATAGTTTGAAAACGTATAATATATAGTTTTTAAAAATA
GTTTTGAAAACGTATAATATATAGTTTTTAAAAACAGTTTTGAAAACATATAATATATAATTTTC
AAAACGGGTTT
Found at i:42733 original size:36 final size:36
Alignment explanation
Indices: 42376--42746 Score: 389
Period size: 36 Copynumber: 10.4 Consensus size: 36
42366 TGTTTTAAAA
*
42376 AAAACGTATAATATATAGTTTTT-AAAATAATTTT-
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* *
42410 AAAAGCGTATAAATATATAGTTTTTCAAAATAGTTTGG
1 AAAA-CGTAT-AATATATAGTTTTTAAAAATAGTTTTG
*
42448 AAAGCGTATAATATATAGTTTTTAAAAATAGTTTTG
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* * ** *
42484 AAAATGTATAATATATAATTTTT-AAAACGGGTTTG
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* ** *
42519 AAAACATATGGTATATAGTTTTT-AAAATAGTTTGG
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
*
42554 AAAATGTATAATATATAGTTTTTAAAAATAGTTTTG
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
*
42590 AAAACGTATAATATATAGTTTTTAAAAACAGTTTTG
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* ** * *
42626 AAAACATAT-ATAATATAG-TTTTCGAAATGGTTTTA
1 AAAACGTATAAT-ATATAGTTTTTAAAAATAGTTTTG
* * * **
42661 AAAACGTATAATATACATTTTTTTAAAGGA-TTTTG
1 AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* **
42696 AAAACGTATAATATATA-TTTTAAAAAACTTTTTTTG
1 AAAACGTATAATATATAGTTTTTAAAAA-TAGTTTTG
*
42732 AAAACATATAATATA
1 AAAACGTATAATATA
42747 ATACTATATA
Statistics
Matches: 278, Mismatches: 49, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
34 11 0.04
35 105 0.38
36 145 0.52
37 14 0.05
38 3 0.01
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (36 bp):
AAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
Found at i:42737 original size:106 final size:106
Alignment explanation
Indices: 42376--42741 Score: 416
Period size: 106 Copynumber: 3.4 Consensus size: 106
42366 TGTTTTAAAA
* * * * *
42376 AAAACGTATAATATATAGTTTTTAAAATAATTTT-AAAAGCGTATAAATATATAGTTTTTCAAAA
1 AAAACGTATAATATATAGTTTTAAAAACAGTTTTGAAAA-CATATATA-ATATAG-TTTTCAAAA
*
42440 TAGTTTGGAAAGCGTATAATATATAGTTTTTAAAAATAGTTTTG
63 TAGTTTGGAAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* * * * * * *
42484 AAAATGTATAATATATAATTTTTAAAACGGGTTTGAAAACATATGGT-ATATAGTTTTTAAAATA
1 AAAACGTATAATATATAGTTTTAAAAACAGTTTTGAAAACATAT-ATAATATAGTTTTCAAAATA
*
42548 GTTTGGAAAATGTATAATATATAGTTTTTAAAAATAGTTTTG
65 GTTTGGAAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
* *
42590 AAAACGTATAATATATAGTTTTTAAAAACAGTTTTGAAAACATATATAATATAGTTTTCGAAATG
1 AAAACGTATAATATATAG-TTTTAAAAACAGTTTTGAAAACATATATAATATAGTTTTCAAAATA
** * * * **
42655 GTTTTAAAAACGTATAATATACATTTTTTTAAAGGA-TTTTG
65 GTTTGGAAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
**
42696 AAAACGTATAATATATA-TTTTAAAAAACTTTTTTTGAAAACATATA
1 AAAACGTATAATATATAGTTTT-AAAAAC-AGTTTTGAAAACATATA
42742 ATATAATACT
Statistics
Matches: 221, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
104 4 0.02
105 6 0.03
106 104 0.47
107 71 0.32
108 32 0.14
109 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (106 bp):
AAAACGTATAATATATAGTTTTAAAAACAGTTTTGAAAACATATATAATATAGTTTTCAAAATAG
TTTGGAAAACGTATAATATATAGTTTTTAAAAATAGTTTTG
Found at i:42786 original size:4 final size:4
Alignment explanation
Indices: 42777--42815 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
42767 TTACATATTA
42777 TTAT TTAT TTAT TTAT TTCAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TT
42816 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:42799 original size:17 final size:17
Alignment explanation
Indices: 42779--42828 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
42769 ACATATTATT
42779 ATTTATTTATTTATTTC
1 ATTTATTTATTTATTTC
42796 ATTTATTTATTTATTT-
1 ATTTATTTATTTATTTC
*
42812 ATTT-TTATTTTTATTTC
1 ATTTATT-TATTTATTTC
42829 GATCAAGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
17 16 0.53
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTATTTC
Found at i:42805 original size:25 final size:25
Alignment explanation
Indices: 42764--42815 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
42754 ATAGTTGTTA
42764 TTATTACATATTATTATTTATTTAT
1 TTATTACATATTATTATTTATTTAT
*
42789 TTATTTCAT-TTATTTATTTATTTAT
1 TTATTACATATTA-TTATTTATTTAT
42814 TT
1 TT
42816 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTACATATTATTATTTATTTAT
Found at i:43929 original size:16 final size:17
Alignment explanation
Indices: 43894--43932 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
43884 AATCCTTAAA
43894 TTTTTATTTATTTATCT
1 TTTTTATTTATTTATCT
43911 TTTTTATTGT-TTTAT-T
1 TTTTTATT-TATTTATCT
43927 TTTTTA
1 TTTTTA
43933 ATTTCTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 13 0.62
18 1 0.05
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTATTTATTTATCT
Found at i:43936 original size:9 final size:8
Alignment explanation
Indices: 43894--43932 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
43884 AATCCTTAAA
43894 TTTTTATT
1 TTTTTATT
*
43902 TATTTATCT
1 TTTTTAT-T
43911 TTTTTATT
1 TTTTTATT
*
43919 GTTTTATT
1 TTTTTATT
43927 TTTTTA
1 TTTTTA
43933 ATTTCTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTTTATT
Found at i:56401 original size:36 final size:35
Alignment explanation
Indices: 56283--56683 Score: 431
Period size: 36 Copynumber: 11.3 Consensus size: 35
56273 TTTGCAAAAC
56283 ACGTATAATATATAGTTTTTAAAATAGTTTT-AGAA
1 ACGTATAATATATAGTTTTTAAAATAGTTTTGA-AA
*
56318 ACGTATAATATATAGTTTTTAAAA-CGATTTTGAAA
1 ACGTATAATATATAGTTTTTAAAATAG-TTTTGAAA
* * *
56353 ACATATAGTATATAGTTTTTCAAAATAGTTTGGAAA
1 ACGTATAATATATAGTTTTT-AAAATAGTTTTGAAA
*
56389 ATGTATAATATATAGTTTTTAAAAATAGTTTTGAAA
1 ACGTATAATATATAGTTTTT-AAAATAGTTTTGAAA
** *
56425 ACGTATAATATATAGTTTTTAAAACGGTTTCGAAA
1 ACGTATAATATATAGTTTTTAAAATAGTTTTGAAA
* * *
56460 ACATATAGTATATAGTTTTTTAAAATAGTTTGGAAA
1 ACGTATAATATATAG-TTTTTAAAATAGTTTTGAAA
*
56496 ACGTATAATATATATGTTTTAAAAATAGTTTTGAAA
1 ACGTATAATATATA-GTTTTTAAAATAGTTTTGAAA
*
56532 ACATATAATATATAGTTTTTTAAAA-ACGGTTTTGAAA
1 ACGTATAATATATAG-TTTTTAAAATA--GTTTTGAAA
* * **
56569 ACATAT-ATAATATAGTTTTCAAAACGGTTTTGAAA
1 ACGTATAAT-ATATAGTTTTTAAAATAGTTTTGAAA
*
56604 ATGTATAATATAT-GTTTTT-AAAT-GATTTTGAAA
1 ACGTATAATATATAGTTTTTAAAATAG-TTTTGAAA
** * *
56637 ACGTATAATATATA-TTTAAAAAACATTTTTCGAAA
1 ACGTATAATATATAGTTTTTAAAATAGTTTT-GAAA
*
56672 ACATATAATATA
1 ACGTATAATATA
56684 ATACTATATA
Statistics
Matches: 312, Mismatches: 37, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
32 1 0.00
33 26 0.08
34 13 0.04
35 107 0.34
36 142 0.46
37 23 0.07
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (35 bp):
ACGTATAATATATAGTTTTTAAAATAGTTTTGAAA
Found at i:56427 original size:107 final size:106
Alignment explanation
Indices: 56285--56683 Score: 544
Period size: 107 Copynumber: 3.8 Consensus size: 106
56275 TGCAAAACAC
56285 GTATAATATATAGTTTTTAAAATAGTTTT-AGAAACGTATAATATATAGTTTTTAAAACGATTTT
1 GTATAATATATAGTTTTTAAAATAGTTTTGA-AAACGTATAATATATAGTTTTTAAAACGATTTT
56349 GAAAACATATAGTATATAGTTTTTCAAAATAGTTTGGAAAAT
65 GAAAACATATAGTATATAGTTTTTCAAAATAGTTTGGAAAAT
* *
56391 GTATAATATATAGTTTTTAAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACGGTTTC
1 GTATAATATATAGTTTTT-AAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACGATTTT
* *
56456 GAAAACATATAGTATATAGTTTTTTAAAATAGTTTGGAAAAC
65 GAAAACATATAGTATATAGTTTTTCAAAATAGTTTGGAAAAT
* * *
56498 GTATAATATATATGTTTTAAAAATAGTTTTGAAAACATATAATATATAGTTTTTTAAAAACGGTT
1 GTATAATATATA-GTTTTTAAAATAGTTTTGAAAACGTATAATATATAG-TTTTT-AAAACGATT
** *
56563 TTGAAAACATATA-TAATATAG-TTTTCAAAACGGTTTTGAAAAT
63 TTGAAAACATATAGT-ATATAGTTTTTCAAAATAGTTTGGAAAAT
**
56606 GTATAATATAT-GTTTTT-AAAT-GATTTTGAAAACGTATAATATATA-TTTAAAAAAC-ATTTT
1 GTATAATATATAGTTTTTAAAATAG-TTTTGAAAACGTATAATATATAGTTTTTAAAACGA-TTT
*
56666 TCGAAAACATATAATATA
64 T-GAAAACATATAGTATA
56684 ATACTATATA
Statistics
Matches: 266, Mismatches: 17, Indels: 23
0.87 0.06 0.08
Matches are distributed among these distances:
102 9 0.03
103 17 0.06
104 2 0.01
105 25 0.09
106 23 0.09
107 123 0.46
108 40 0.15
109 27 0.10
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (106 bp):
GTATAATATATAGTTTTTAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACGATTTTG
AAAACATATAGTATATAGTTTTTCAAAATAGTTTGGAAAAT
Found at i:56734 original size:13 final size:13
Alignment explanation
Indices: 56708--56759 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
56698 TTATTATTAC
56708 ATTTTA-TTATTTT
1 ATTTTATTTA-TTT
56721 ATTTTATTTATTT
1 ATTTTATTTATTT
*
56734 ATTTCATTT-TTT
1 ATTTTATTTATTT
*
56746 ATTTATTTTTATTT
1 ATTT-TATTTATTT
56760 TTATTTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 7 0.21
13 20 0.61
14 6 0.18
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:56760 original size:16 final size:16
Alignment explanation
Indices: 56709--56765 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
56699 TATTATTACA
56709 TTTTA-TTA-TTTTA-
1 TTTTATTTATTTTTAT
56722 TTTTATTTATTTATTTCATT
1 TTTTATTTA-TT-TTT-A-T
56742 TTTTATTTATTTTTAT
1 TTTTATTTATTTTTAT
56758 TTTTATTT
1 TTTTATTT
56766 TGGAATAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
16 10 0.27
17 4 0.11
18 4 0.11
19 2 0.05
20 9 0.24
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTATTTTTAT
Found at i:56762 original size:12 final size:11
Alignment explanation
Indices: 56709--56766 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 11
56699 TATTATTACA
56709 TTTTATTATTTT
1 TTTTATT-TTTT
56721 ATTTTATTTATTT
1 -TTTTATTT-TTT
*
56734 ATTTCATTTTTT
1 -TTTTATTTTTT
*
56746 ATTTATTTTTAT
1 TTTTATTTTT-T
56758 TTTTATTTT
1 TTTTATTTT
56767 GGAATAGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 8 0.21
12 13 0.33
13 18 0.46
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:58050 original size:5 final size:5
Alignment explanation
Indices: 58042--58089 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
58032 TAGTTTTTTC
* * *
58042 ATTAT ATTAT ATTTT ATTTT ATTTT ATT-T CATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT -ATTAT ATTAT ATTAT ATT
58090 TTTCTCTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
4 1 0.03
5 38 0.95
6 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (5 bp):
ATTAT
Found at i:58064 original size:10 final size:10
Alignment explanation
Indices: 58009--58091 Score: 51
Period size: 10 Copynumber: 8.3 Consensus size: 10
57999 TACTTTCTTC
*
58009 TTTATTTTTT
1 TTTATTTTAT
* *
58019 TCTTTTTTTAA
1 T-TTATTTTAT
*
58030 TTTAGTTT-T
1 TTTATTTTAT
* *
58039 TTCATTATAT
1 TTTATTTTAT
*
58049 TATATTTTAT
1 TTTATTTTAT
58059 TTTATTTTAT
1 TTTATTTTAT
* *
58069 TTCATTATAT
1 TTTATTTTAT
* *
58079 TATATTATAT
1 TTTATTTTAT
58089 TTT
1 TTT
58092 TCTCTTTTAA
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
9 5 0.09
10 41 0.77
11 7 0.13
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:58074 original size:30 final size:29
Alignment explanation
Indices: 58024--58091 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
58014 TTTTTTCTTT
*
58024 TTTTAATTTAGTTTTTTCATTATATTATA
1 TTTTATTTTAGTTTTTTCATTATATTATA
*
58053 TTTTATTTTATTTTATTTCATTATATTATA
1 TTTTATTTTAGTTT-TTTCATTATATTATA
*
58083 TTATATTTT
1 TTTTATTTT
58092 TCTCTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTTATTTTAGTTTTTTCATTATATTATA
Found at i:60392 original size:13 final size:14
Alignment explanation
Indices: 60369--60406 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
60359 AGGGTTAAAG
60369 AATAGAATAAAATAA
1 AATA-AATAAAATAA
*
60384 GA-AAATAAAATAA
1 AATAAATAAAATAA
60397 AATAAATAAA
1 AATAAATAAA
60407 GAGTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 11 0.55
14 8 0.40
15 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (14 bp):
AATAAATAAAATAA
Found at i:61772 original size:5 final size:4
Alignment explanation
Indices: 61726--61770 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
61716 GAAAAAATAA
* *
61726 AAAT GAAT AAAT AAAT AAAT AAAT AAAT GAAAAG AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAA
61771 ATGTATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 32 0.91
6 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:61980 original size:64 final size:64
Alignment explanation
Indices: 61929--62079 Score: 197
Period size: 64 Copynumber: 2.4 Consensus size: 64
61919 TTTTGAAAAG
* *
61929 TTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTC-AAGACTATATATTGTATATATA
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG-TTTCAAAAACTATATATTGTATATAAA
* * *
61993 TTTTCAAAAACTATATATTATATATTTTTTCAAAATGTTTCAAAAACTATATA-TATATATATA
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTCAAAAACTATATATTGTATATAAA
*
62056 TATTCAAAAA--A-AT-TTATATATATT
1 TTTTCAAAAACTATATATTATATATATT
62080 AAATAGAACC
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
59 10 0.12
60 2 0.02
61 1 0.01
63 22 0.27
64 46 0.57
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (64 bp):
TTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTCAAAAACTATATATTGTATATAAA
Found at i:61989 original size:36 final size:37
Alignment explanation
Indices: 61792--62064 Score: 279
Period size: 36 Copynumber: 7.6 Consensus size: 37
61782 TTTTAAAATG
* *
61792 ATATTATATATATTTTCAAAAAATGCTTTC-AAAACCAT
1 ATATTATATATATTTTC--AAAATGTTTTCAAAAACTAT
* * *
61830 ATA-T-TATATGTGTTCAAAAATGTTTACAAAAACTAT
1 ATATTATATATATTTTC-AAAATGTTTTCAAAAACTAT
61866 ATATTATATATATATTTTCAAAATGTTTTCAAAAAACTAT
1 ATA-T-TATATATATTTTCAAAATGTTTTC-AAAAACTAT
*
61906 ATATTATATATATTTTTGAAAA-GTTTTCAAAAACTAT
1 ATATTATATATA-TTTTCAAAATGTTTTCAAAAACTAT
*
61943 ATATTATATATATTTTCAAAATGTTTTC-AAGACTAT
1 ATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
*
61979 ATATTGTATATA---T----A--TTTTCAAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
*
62007 ATATTATATATTTTTTCAAAATG-TTTCAAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
*
62043 ATATATATATATATATTCAAAA
1 ATAT-TATATATATTTTCAAAA
62065 AAATTTATAT
Statistics
Matches: 199, Mismatches: 17, Indels: 39
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.03
28 17 0.09
29 1 0.01
31 1 0.01
33 1 0.01
35 11 0.06
36 62 0.31
37 43 0.22
38 17 0.09
39 20 0.10
40 21 0.11
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATTATATATATTTTCAAAATGTTTTCAAAAACTAT
Found at i:62014 original size:26 final size:28
Alignment explanation
Indices: 61966--62027 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
61956 TTTCAAAATG
*
61966 TTTTC-AAGACTATATATTGTATATATA
1 TTTTCAAAAACTATATATTGTATATATA
*
61993 TTTTCAAAAACTATATA-T-TATATATT
1 TTTTCAAAAACTATATATTGTATATATA
62019 TTTTCAAAA
1 TTTTCAAAA
62028 TGTTTCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 16 0.50
27 6 0.19
28 10 0.31
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTTCAAAAACTATATATTGTATATATA
Done.