Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001286.1 Hibiscus syriacus cultivar Beakdansim tig00002520_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: 78628
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:13627 original size:20 final size:21
Alignment explanation
Indices: 13588--13759 Score: 210
Period size: 20 Copynumber: 8.4 Consensus size: 21
13578 TTTCTAGCTG
* *
13588 AGAGTATCGAAACTTTTCCCA
1 AGAGTATCCATACTTTTCCCA
13609 AGAGTA-CCGATAC-TTTCCCA
1 AGAGTATCC-ATACTTTTCCCA
*
13629 AGTGTATCCATACTTTTCCCA
1 AGAGTATCCATACTTTTCCCA
* * *
13650 AGAGTATACGTAC-TTTCCAA
1 AGAGTATCCATACTTTTCCCA
* *
13670 AGAGTATTCATACTTTTCTCA
1 AGAGTATCCATACTTTTCCCA
13691 AGAGTATCCATAC-TTTCCCA
1 AGAGTATCCATACTTTTCCCA
* *
13711 ATAGTATCCATGCTTTT-CCA
1 AGAGTATCCATACTTTTCCCA
13731 AGAGTATCCATACTTTTCCCA
1 AGAGTATCCATACTTTTCCCA
13752 AGAGTATC
1 AGAGTATC
13760 GACATTACTC
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
20 69 0.54
21 59 0.46
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (21 bp):
AGAGTATCCATACTTTTCCCA
Found at i:13648 original size:41 final size:41
Alignment explanation
Indices: 13588--13759 Score: 222
Period size: 41 Copynumber: 4.2 Consensus size: 41
13578 TTTCTAGCTG
* *
13588 AGAGTATCGAAACTTTTCCCAAGAGTA-CCGATACTTTCCCA
1 AGAGTATCCATACTTTTCCCAAGAGTATCC-ATACTTTCCCA
* * * *
13629 AGTGTATCCATACTTTTCCCAAGAGTATACGTACTTTCCAA
1 AGAGTATCCATACTTTTCCCAAGAGTATCCATACTTTCCCA
* *
13670 AGAGTATTCATACTTTTCTCAAGAGTATCCATACTTTCCCA
1 AGAGTATCCATACTTTTCCCAAGAGTATCCATACTTTCCCA
* *
13711 ATAGTATCCATGCTTTT-CCAAGAGTATCCATACTTTTCCCA
1 AGAGTATCCATACTTTTCCCAAGAGTATCCATAC-TTTCCCA
13752 AGAGTATC
1 AGAGTATC
13760 GACATTACTC
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 15 0.13
41 96 0.86
42 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (41 bp):
AGAGTATCCATACTTTTCCCAAGAGTATCCATACTTTCCCA
Found at i:20790 original size:2 final size:2
Alignment explanation
Indices: 20783--20813 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20773 TCTAGTTGTC
20783 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20814 TTAATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20836 original size:25 final size:26
Alignment explanation
Indices: 20808--20856 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
20798 TATATATATA
*
20808 TAATA-TTTAATAATTTAATTTTTTT
1 TAATATTTTAATAATTAAATTTTTTT
*
20833 TAATATTTTTATAATTAAATTTTT
1 TAATATTTTAATAATTAAATTTTT
20857 GAATATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TAATATTTTAATAATTAAATTTTTTT
Found at i:20880 original size:16 final size:15
Alignment explanation
Indices: 20831--20882 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
20821 TTTAATTTTT
20831 TTTAATATTTTTATA
1 TTTAATATTTTTATA
*
20846 ATTAA-ATTTTTGAATA
1 TTTAATATTTTT--ATA
20862 TTTGAATATTTTTATA
1 TTT-AATATTTTTATA
20878 TTTAA
1 TTTAA
20883 ACTTTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
16 11 0.35
17 2 0.06
18 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
TTTAATATTTTTATA
Found at i:20904 original size:31 final size:30
Alignment explanation
Indices: 20810--20911 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 30
20800 TATATATATA
*
20810 ATATTTAATAATTTAATTTTTTTTAATATTTTT
1 ATATTTAA-AATTTAA--TTTTTAAATATTTTT
* * * *
20843 ATAATTAAATTTTTGAATATTTGAATATTTTT
1 ATATTTAAA-ATTT-AATTTTTAAATATTTTT
*
20875 ATATTTAAACTTTAATTTTTAAAATATTTTT
1 ATATTTAAAATTTAATTTTT-AAATATTTTT
*
20906 TTATTT
1 ATATTT
20912 TTTCAAAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
30 6 0.11
31 17 0.30
32 22 0.39
33 10 0.18
34 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (30 bp):
ATATTTAAAATTTAATTTTTAAATATTTTT
Found at i:21686 original size:23 final size:23
Alignment explanation
Indices: 21656--21706 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
21646 GCTTTGCAAT
*
21656 GACTTCTGATAGGAAAGTATAGA
1 GACTTCTGATAAGAAAGTATAGA
21679 GACTTCTGATAAGAAAGTATAGA
1 GACTTCTGATAAGAAAGTATAGA
21702 GACTT
1 GACTT
21707 AAAATCAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (23 bp):
GACTTCTGATAAGAAAGTATAGA
Found at i:23569 original size:23 final size:24
Alignment explanation
Indices: 23520--23577 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
23510 CATTTTAATC
23520 AAAATATTAATTATTAAAATATTT-
1 AAAATA-TAATTATTAAAATATTTA
* *
23544 AAAATATATTTATTAATAT-TTCTA
1 AAAATATAATTATTAAAATATT-TA
23568 AAAATATAAT
1 AAAATATAAT
23578 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.07
23 12 0.41
24 15 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATATAATTATTAAAATATTTA
Found at i:23603 original size:27 final size:27
Alignment explanation
Indices: 23543--23635 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 27
23533 TTAAAATATT
*
23543 TAAAAT-ATATTTATTAATATTTCTAA
1 TAAAATAATATTTATTAATATTTATAA
*
23569 -AAATATAATATTTTTTTAATA-TTATAA
1 TAAA-ATAATA-TTTATTAATATTTATAA
23596 TAAAATAATCA---ATT-ATA-TTATAA
1 TAAAATAAT-ATTTATTAATATTTATAA
*
23619 TAATATAATATATTATT
1 TAAAATAATAT-TTATT
23636 TTTTATTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
22 1 0.02
23 17 0.31
24 2 0.04
25 3 0.06
26 5 0.09
27 13 0.24
28 13 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TAAAATAATATTTATTAATATTTATAA
Found at i:23737 original size:19 final size:18
Alignment explanation
Indices: 23713--23780 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
23703 ATATTATTAA
23713 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
*
23732 ATTATT-AT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
23749 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
23771 ATT-TTAATAA
1 ATTATTAATAA
23781 AGATATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
16 1 0.03
17 9 0.22
18 4 0.10
19 13 0.32
20 3 0.08
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:23795 original size:23 final size:23
Alignment explanation
Indices: 23775--23819 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
23765 AATAATATTT
23775 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
23798 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
23820 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:24150 original size:14 final size:14
Alignment explanation
Indices: 24133--24163 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24123 CATTTTACGA
*
24133 AAAAAATTTTCCGG
1 AAAAAATTTTCCAG
24147 AAAAAATTTTCCAG
1 AAAAAATTTTCCAG
24161 AAA
1 AAA
24164 TGTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (14 bp):
AAAAAATTTTCCAG
Found at i:24194 original size:14 final size:14
Alignment explanation
Indices: 24175--24254 Score: 117
Period size: 14 Copynumber: 5.6 Consensus size: 14
24165 GTAATTTTAT
*
24175 TTTCCAAAATTCAA
1 TTTCCAGAATTCAA
24189 TTTCCAGTAATTC-A
1 TTTCCAG-AATTCAA
24203 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
*
24217 TTTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
24232 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
24246 TTTCCAGAA
1 TTTCCAGAA
24255 AACTAATTAC
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
13 5 0.08
14 37 0.62
15 18 0.30
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:24245 original size:29 final size:29
Alignment explanation
Indices: 24173--24252 Score: 144
Period size: 28 Copynumber: 2.8 Consensus size: 29
24163 ATGTAATTTT
*
24173 ATTTTCCAAAATTCAATTTCCAGTAATTC
1 ATTTTCCAGAATTCAATTTCCAGTAATTC
24202 A-TTTCCAGAATTCAATTTCCAGTAATTC
1 ATTTTCCAGAATTCAATTTCCAGTAATTC
24230 ATTTTCCAGAATTCAATTTCCAG
1 ATTTTCCAGAATTCAATTTCCAG
24253 AAAACTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 27 0.55
29 22 0.45
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (29 bp):
ATTTTCCAGAATTCAATTTCCAGTAATTC
Found at i:26653 original size:29 final size:28
Alignment explanation
Indices: 26613--26774 Score: 173
Period size: 28 Copynumber: 5.6 Consensus size: 28
26603 ATCACTTAAT
* *
26613 TAAGTACATAAAATATTTTTTAGTCAAAA
1 TAAGTACCTAAAGTATTTTTT-GTCAAAA
* *
26642 TAAATATCTAAAGTTATTTTTTTGGTCAAAA
1 TAAGTACCTAAAG-TA-TTTTTT-GTCAAAA
* * *
26673 TAGGTACCCAAAGTATTTTATGTCAAAA
1 TAAGTACCTAAAGTATTTTTTGTCAAAA
26701 TAAGTACCTAAAGTTATTTTTTGTCAAAA
1 TAAGTACCTAAAG-TATTTTTTGTCAAAA
* *
26730 T-AGTTAACTAAAGTATTTTATGTCAAAA
1 TAAG-TACCTAAAGTATTTTTTGTCAAAA
*
26758 TAGGTACCTAAAGTATT
1 TAAGTACCTAAAGTATT
26775 CAAGATTTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
28 47 0.42
29 38 0.34
30 4 0.04
31 22 0.20
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTTGTCAAAA
Found at i:26748 original size:57 final size:59
Alignment explanation
Indices: 26630--26771 Score: 209
Period size: 57 Copynumber: 2.5 Consensus size: 59
26620 ATAAAATATT
* * *
26630 TTTTA-GTCAAAATAAATATCTAAAGTTATTTTTTTGGTCAAAATAGGTACCCAAAGTA
1 TTTTATGTCAAAATAAGTACCTAAAGTTATTTTTTTGGTCAAAATAGGTAACCAAAGTA
* *
26688 TTTTATGTCAAAATAAGTACCTAAAGTTA-TTTTTT-GTCAAAATAGTTAACTAAAGTA
1 TTTTATGTCAAAATAAGTACCTAAAGTTATTTTTTTGGTCAAAATAGGTAACCAAAGTA
*
26745 TTTTATGTCAAAATAGGTACCTAAAGT
1 TTTTATGTCAAAATAAGTACCTAAAGT
26772 ATTCAAGATT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
57 45 0.58
58 11 0.14
59 21 0.27
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (59 bp):
TTTTATGTCAAAATAAGTACCTAAAGTTATTTTTTTGGTCAAAATAGGTAACCAAAGTA
Found at i:32865 original size:18 final size:18
Alignment explanation
Indices: 32842--32886 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
32832 GAAATGGTCA
32842 TCGTCAGTTAAAATGGGT
1 TCGTCAGTTAAAATGGGT
32860 TCGTCAGTTAAAATGGGT
1 TCGTCAGTTAAAATGGGT
*
32878 TCCTCAGTT
1 TCGTCAGTT
32887 TCTTTATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (18 bp):
TCGTCAGTTAAAATGGGT
Found at i:33900 original size:30 final size:31
Alignment explanation
Indices: 33839--33909 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
33829 GTTATAAGAG
* *
33839 CTATGTGATAAAAGTATTGAAAATGATATGT
1 CTATGTGATAAAAGTATAGAAAATAATATGT
33870 CTATGTGAT-AAAGATATAG-AAATAATATGT
1 CTATGTGATAAAAG-TATAGAAAATAATATGT
*
33900 CTATGAGATA
1 CTATGTGATA
33910 CATTATGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 22 0.63
31 13 0.37
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (31 bp):
CTATGTGATAAAAGTATAGAAAATAATATGT
Found at i:34778 original size:21 final size:21
Alignment explanation
Indices: 34752--34814 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
34742 GATATTTTTT
34752 GTGCATCGGTACACTATAGCA
1 GTGCATCGGTACACTATAGCA
34773 GTGCATCGGTACACTATAGCA
1 GTGCATCGGTACACTATAGCA
* *
34794 ATGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTATAGCA
34815 CTGTTTCATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
GTGCATCGGTACACTATAGCA
Found at i:34849 original size:22 final size:23
Alignment explanation
Indices: 34814--34857 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
34804 ACACTGTAGC
*
34814 ACTGTTTCATGGTAATGTTCATT
1 ACTGTTTCACGGTAATGTTCATT
*
34837 ACTG-TTCACGGTATTGTTCAT
1 ACTGTTTCACGGTAATGTTCAT
34858 ACCGTATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (23 bp):
ACTGTTTCACGGTAATGTTCATT
Found at i:39181 original size:53 final size:54
Alignment explanation
Indices: 39079--39186 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 54
39069 AAAAGTATCT
* * *
39079 AATAAATTAAAATAACAAACCATTATGGGTGGAACTCCTATAAT-GAAAAATAA
1 AATAAAATAAAATAAAAAACCATTATGGGTGGAACTCCTATAATAAAAAAATAA
* * * *
39132 AATAAAATAAAATAAAAAATCTTTATGGGTGGAACTGCTATATTAAAAAAATAA
1 AATAAAATAAAATAAAAAACCATTATGGGTGGAACTCCTATAATAAAAAAATAA
39186 A
1 A
39187 TGAAATCACT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 38 0.81
54 9 0.19
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (54 bp):
AATAAAATAAAATAAAAAACCATTATGGGTGGAACTCCTATAATAAAAAAATAA
Found at i:44283 original size:41 final size:42
Alignment explanation
Indices: 44230--44341 Score: 99
Period size: 41 Copynumber: 2.7 Consensus size: 42
44220 GTGTTTTTGT
44230 ACAAAC-TCCACTAAGACT-TGA-ACTTTAGTAGCATTTTAAAC
1 ACAAACGTCCACTAA-A-TATGATACTTTAGTAGCATTTTAAAC
* * * *
44271 ACAAACGT-CACTAAATATTATACTTTAGTGGCGTTTTAAGC
1 ACAAACGTCCACTAAATATGATACTTTAGTAGCATTTTAAAC
* * *
44312 ACAAACG-CCGCCAAAATATCATACTTTAGT
1 ACAAACGTCC-ACTAAATATGATACTTTAGT
44342 GCCGTTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 1 0.02
40 3 0.05
41 37 0.63
42 18 0.31
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (42 bp):
ACAAACGTCCACTAAATATGATACTTTAGTAGCATTTTAAAC
Found at i:44340 original size:42 final size:41
Alignment explanation
Indices: 44251--44349 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
44241 TAAGACTTGA
* * * * *
44251 ACTTTAGTAGCATTTTAAACACAAACGTCACTAAATATTAT
1 ACTTTAGTGGCGTTTTAAACACAAACGCCACAAAATATCAT
* *
44292 ACTTTAGTGGCGTTTTAAGCACAAACGCCGCCAAAATATCAT
1 ACTTTAGTGGCGTTTTAAACACAAACGCC-ACAAAATATCAT
*
44334 ACTTTAGTGCCGTTTT
1 ACTTTAGTGGCGTTTT
44350 TTATATAAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 25 0.51
42 24 0.49
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTAAACACAAACGCCACAAAATATCAT
Found at i:44460 original size:42 final size:41
Alignment explanation
Indices: 44414--44516 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
44404 TATACAAATA
*
44414 CCGCTAAAGACTCGTACTTTAATGACGTTTTAAGCACAAACG
1 CCGCTAAAGACTCGTACTTTAATGACG-TTTAAGCAAAAACG
* * * *
44456 CCGCTATATACTCGTACTTTAGTGGCGTTTAAGCAAAAACG
1 CCGCTAAAGACTCGTACTTTAATGACGTTTAAGCAAAAACG
** *
44497 CAACCAAAGACTCGTACTTT
1 CCGCTAAAGACTCGTACTTT
44517 TCATTTTTCC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 28 0.55
42 23 0.45
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (41 bp):
CCGCTAAAGACTCGTACTTTAATGACGTTTAAGCAAAAACG
Found at i:44546 original size:16 final size:15
Alignment explanation
Indices: 44513--44543 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44503 AAGACTCGTA
44513 CTTTTCATTTTTCCC
1 CTTTTCATTTTTCCC
44528 CTTTTCATTTTTCCC
1 CTTTTCATTTTTCCC
44543 C
1 C
44544 CTTCACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.58
Consensus pattern (15 bp):
CTTTTCATTTTTCCC
Found at i:44548 original size:14 final size:15
Alignment explanation
Indices: 44516--44548 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44506 ACTCGTACTT
*
44516 TTCATTTTTCCCCTT
1 TTCATTTTTCCCCTC
44531 TTCATTTTTCCCC-C
1 TTCATTTTTCCCCTC
44545 TTCA
1 TTCA
44549 CCTATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCATTTTTCCCCTC
Found at i:47357 original size:21 final size:21
Alignment explanation
Indices: 47331--47392 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
47321 CTTTGATTTA
*
47331 TTATTATTGATTTCAAGTTTC
1 TTATTATAGATTTCAAGTTTC
* *
47352 TTATTATGGATTTCAAGTTTG
1 TTATTATAGATTTCAAGTTTC
* *
47373 TTGTTATAGATGTCAAGTTT
1 TTATTATAGATTTCAAGTTT
47393 ATTGGATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (21 bp):
TTATTATAGATTTCAAGTTTC
Found at i:47697 original size:44 final size:44
Alignment explanation
Indices: 47603--47701 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
47593 TTTTATATTC
* * *
47603 ACAAACACCACTATACGACAAAACATTTAGCGACGTTTTTTGGA
1 ACAAACGCCACTATACGACAAAACATTTAACGACGTTTTTGGGA
* * *
47647 ACAAACGCCACTATATGTCAGAACATTTAACGACGTTTTTGGGA
1 ACAAACGCCACTATACGACAAAACATTTAACGACGTTTTTGGGA
47691 TA-AAACGCCAC
1 -ACAAACGCCAC
47702 AAAAGAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 47 0.98
45 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (44 bp):
ACAAACGCCACTATACGACAAAACATTTAACGACGTTTTTGGGA
Found at i:60342 original size:131 final size:131
Alignment explanation
Indices: 60077--60324 Score: 410
Period size: 131 Copynumber: 1.9 Consensus size: 131
60067 TCAAGACAAT
* * *
60077 TTTTAGGCCTAGTCAAAGTACATACGTATATGAAGTGTTGAAAATGTTCGACATAAAAAATCGTA
1 TTTTAGGCCTAGTCAAAATACATACATATATAAAGTGTTGAAAATGTTCGACATAAAAAATCGTA
* *
60142 AAATGATTTTCAAAATTTATTTTTTAAAAATATTATTCGTTTTTGATGGAATCAAAACGAATAAT
66 AAATGATTTTCAAAAATTATTTTTTAAAAATATTATTCGTTTTTGAAGGAATCAAAACGAATAAT
60207 A
131 A
* *
60208 TTTTAGGCCTAGTCAAAATATATACATATATAAAGTGTTGAAAATGTTCGACATAGAAAATCGTA
1 TTTTAGGCCTAGTCAAAATACATACATATATAAAGTGTTGAAAATGTTCGACATAAAAAATCGTA
*
60273 AAATGATTTTCAAAAATTATTTTTTAAAATTATTA-TCG-TTTTGAAGGAATCA
66 AAATGATTTTCAAAAATTATTTTTTAAAAATATTATTCGTTTTTGAAGGAATCA
60325 TTTTTCAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 13 0.12
130 3 0.03
131 93 0.85
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (131 bp):
TTTTAGGCCTAGTCAAAATACATACATATATAAAGTGTTGAAAATGTTCGACATAAAAAATCGTA
AAATGATTTTCAAAAATTATTTTTTAAAAATATTATTCGTTTTTGAAGGAATCAAAACGAATAAT
A
Found at i:61166 original size:2 final size:2
Alignment explanation
Indices: 61161--61185 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61151 AAAAAAAGTT
61161 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
61186 TACTTTTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67002 original size:21 final size:21
Alignment explanation
Indices: 66976--67029 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
66966 GACTCGCTGT
66976 GGAACGAAAGATATTCTTGAG
1 GGAACGAAAGATATTCTTGAG
66997 GGAACGAAAGATATTCTTGAG
1 GGAACGAAAGATATTCTTGAG
*
67018 GGATCGAAAGAT
1 GGAACGAAAGAT
67030 TAAGTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (21 bp):
GGAACGAAAGATATTCTTGAG
Found at i:69286 original size:34 final size:34
Alignment explanation
Indices: 69248--69349 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
69238 ATCCGAAAAC
69248 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
1 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
69282 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
1 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
69316 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
1 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
69350 TTAAAGCTGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.35
Consensus pattern (34 bp):
CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
Found at i:70013 original size:16 final size:16
Alignment explanation
Indices: 69972--70049 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 16
69962 GCCAAAAGAG
69972 CTGAATCGAAAGCAAC
1 CTGAATCGAAAGCAAC
* * **
69988 CTAAACCGAAATTAAC
1 CTGAATCGAAAGCAAC
70004 CTGAATCGAAAGCAA-
1 CTGAATCGAAAGCAAC
* * **
70019 TTCGAACCGAAATTAAC
1 CT-GAATCGAAAGCAAC
*
70036 CCGAATCGAAAGCA
1 CTGAATCGAAAGCA
70050 GCCCGAACTG
Statistics
Matches: 43, Mismatches: 17, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
15 1 0.02
16 42 0.98
ACGTcount: A:0.45, C:0.24, G:0.15, T:0.15
Consensus pattern (16 bp):
CTGAATCGAAAGCAAC
Found at i:70057 original size:32 final size:32
Alignment explanation
Indices: 69974--70118 Score: 114
Period size: 32 Copynumber: 4.5 Consensus size: 32
69964 CAAAAGAGCT
** *
69974 GAATCGAAAGCAACCTAAACCGAAATTAACCT
1 GAATCGAAAGCAACCCGAACCGAAATTAACCC
**
70006 GAATCGAAAGCAATTCGAACCGAAATTAACCC
1 GAATCGAAAGCAACCCGAACCGAAATTAACCC
* * ** *
70038 GAATCGAAAGCAGCCCGAACTGATCTTAACTC
1 GAATCGAAAGCAACCCGAACCGAAATTAACCC
* * *
70070 GAA-CTGAAAGAAACCTGAAAC-AAATTTTAACCC
1 GAATC-GAAAGCAACCCGAACCGAAA--TTAACCC
* *
70103 GATTCAAAAGCAACCC
1 GAATCGAAAGCAACCC
70119 CAATAGAAAT
Statistics
Matches: 85, Mismatches: 24, Indels: 7
0.73 0.21 0.06
Matches are distributed among these distances:
31 2 0.02
32 66 0.78
33 16 0.19
34 1 0.01
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (32 bp):
GAATCGAAAGCAACCCGAACCGAAATTAACCC
Found at i:71005 original size:32 final size:32
Alignment explanation
Indices: 70910--71019 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 32
70900 GGTTGATCCA
* * *
70910 AACCGAAAAATTAACTGATTCGATATTGAA-CC
1 AACCCAAAAATCAACTGATCCGATA-TGAACCC
** * * *
70942 AACCC-AAAATCTAACCAATCTGGTATTAACCC
1 AACCCAAAAATC-AACTGATCCGATATGAACCC
*
70974 GACCCAAAAATCAACTGATCCGATATGAACCC
1 AACCCAAAAATCAACTGATCCGATATGAACCC
* *
71006 TATCCAAAAATCAA
1 AACCCAAAAATCAA
71020 TCGGTCTAAT
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
31 8 0.14
32 45 0.76
33 6 0.10
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (32 bp):
AACCCAAAAATCAACTGATCCGATATGAACCC
Found at i:71881 original size:64 final size:64
Alignment explanation
Indices: 71802--71954 Score: 234
Period size: 64 Copynumber: 2.4 Consensus size: 64
71792 CTTACCAACT
* * * *
71802 TGGATCTCTCGGCGTCTTCCATGCACGCTCGGGGGAATGTTTGGCGTCTTCAAGCATGGGAAAA
1 TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGGAAAA
*
71866 TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGTAAAA
1 TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGGAAAA
** *
71930 TATATCTCTCGGTGTCTTCCATGCA
1 TGGATCTCTCGGCGTCTTCCATGCA
71955 ATGGGAACAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (64 bp):
TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGGAAAA
Found at i:72628 original size:11 final size:12
Alignment explanation
Indices: 72600--72630 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
72590 ATTTCATGTA
72600 ATTTTTAGTTGT
1 ATTTTTAGTTGT
72612 ATTTTTAGTTGT
1 ATTTTTAGTTGT
72624 ATTTTTA
1 ATTTTTA
72631 TATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (12 bp):
ATTTTTAGTTGT
Found at i:75683 original size:22 final size:23
Alignment explanation
Indices: 75642--75701 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
75632 TGATATGATT
75642 TAATGATTTACTAATAATTTAATAC
1 TAATGA-TTA-TAATAATTTAATAC
* *
75667 TAATGATT-TAATTATTTGATAC
1 TAATGATTATAATAATTTAATAC
75689 TAATGATTATAAT
1 TAATGATTATAAT
75702 GATTGATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 20 0.62
23 4 0.12
24 2 0.06
25 6 0.19
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (23 bp):
TAATGATTATAATAATTTAATAC
Found at i:75774 original size:33 final size:30
Alignment explanation
Indices: 75734--75811 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 30
75724 ATTTGAACTT
75734 TAATGATTTAATAATGATTACTAATTTTATAAA
1 TAATGATTTAATAATGA-TA-TAA-TTTATAAA
* *
75767 TAATGATTTAAGTATAATGATATGATTTATTAA
1 TAATGATTT-A--ATAATGATATAATTTATAAA
75800 TAATGATTTAAT
1 TAATGATTTAAT
75812 GATTTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
30 2 0.05
32 1 0.03
33 25 0.62
34 3 0.08
35 2 0.05
36 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (30 bp):
TAATGATTTAATAATGATATAATTTATAAA
Found at i:75813 original size:8 final size:8
Alignment explanation
Indices: 75800--75833 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
75790 GATTTATTAA
75800 TAATGATT
1 TAATGATT
75808 TAATGATT
1 TAATGATT
75816 TAAT-A-T
1 TAATGATT
75822 TAATGATT
1 TAATGATT
75830 TAAT
1 TAAT
75834 AATAAGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.21
7 2 0.08
8 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (8 bp):
TAATGATT
Found at i:75813 original size:22 final size:22
Alignment explanation
Indices: 75767--75833 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
75757 ATTTTATAAA
75767 TAATGATTTAAGT-ATAATGA--
1 TAATGATTTAA-TAATAATGATT
*
75787 T-ATGATTTATTAATAATGATT
1 TAATGATTTAATAATAATGATT
*
75808 TAATGATTTAATATTAATGATT
1 TAATGATTTAATAATAATGATT
75830 TAAT
1 TAAT
75834 AATAAGGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.38
20 1 0.03
21 1 0.03
22 22 0.55
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TAATGATTTAATAATAATGATT
Found at i:75824 original size:14 final size:14
Alignment explanation
Indices: 75807--75834 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
75797 TAATAATGAT
75807 TTAATGATTTAATA
1 TTAATGATTTAATA
75821 TTAATGATTTAATA
1 TTAATGATTTAATA
75835 ATAAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAATGATTTAATA
Found at i:75826 original size:55 final size:59
Alignment explanation
Indices: 75741--75871 Score: 150
Period size: 55 Copynumber: 2.3 Consensus size: 59
75731 CTTTAATGAT
* * *
75741 TTAATAATGA-TTACTAATTTTATAAATAATGATTTAAGT-ATAATGA-T-ATGATTT-A
1 TTAATAATGATTTAATAATTTAATAAATAATGATTTAA-TAATAAGGATTAATGATTTGA
* *
75796 TTAATAATGATTTAATGATTTAAT-ATTAATGATTTAATAATAAGGATTAATGATTTGA
1 TTAATAATGATTTAATAATTTAATAAATAATGATTTAATAATAAGGATTAATGATTTGA
*
75854 -TACTAATGATTTAATAAT
1 TTAATAATGATTTAATAAT
75872 AATTTGATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
54 1 0.02
55 28 0.44
56 11 0.17
57 23 0.36
58 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (59 bp):
TTAATAATGATTTAATAATTTAATAAATAATGATTTAATAATAAGGATTAATGATTTGA
Found at i:75836 original size:25 final size:25
Alignment explanation
Indices: 75788--75928 Score: 61
Period size: 25 Copynumber: 5.8 Consensus size: 25
75778 GTATAATGAT
*
75788 ATGATTTATTAATAATGA-TT--TA
1 ATGATTTAATAATAATGATTTAATA
*
75810 ATGATTTAATATTAATGATTTAATA
1 ATGATTTAATAATAATGATTTAATA
* * *
75835 ATAAGGA-TTAATGAT-TTGA--TACTA
1 AT---GATTTAATAATAATGATTTAATA
75859 ATGATTTAATAATAAT--TTGATAATA
1 ATGATTTAATAATAATGATT--TAATA
* * * *
75884 ATGATTTAAAAATGATTGA-ATAACA
1 ATGATTTAATAAT-AATGATTTAATA
*
75909 ATGA-TTACTAATAATGATTT
1 ATGATTTAATAATAATGATTT
75929 GAACTTTAAT
Statistics
Matches: 86, Mismatches: 17, Indels: 30
0.65 0.13 0.23
Matches are distributed among these distances:
21 2 0.02
22 23 0.27
23 7 0.08
24 13 0.15
25 28 0.33
26 5 0.06
27 6 0.07
28 2 0.02
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (25 bp):
ATGATTTAATAATAATGATTTAATA
Found at i:75860 original size:14 final size:13
Alignment explanation
Indices: 75843--75890 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
75833 TAATAAGGAT
75843 TAATGATTTGATA
1 TAATGATTTGATA
75856 CTAATGATTT-A-A
1 -TAATGATTTGATA
*
75868 TAATAATTTGATAA
1 TAATGATTTGAT-A
75882 TAATGATTT
1 TAATGATTT
75891 AAAAATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 1 0.03
14 18 0.62
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (13 bp):
TAATGATTTGATA
Found at i:75861 original size:35 final size:36
Alignment explanation
Indices: 75788--75873 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
75778 GTATAATGAT
* * *
75788 ATGATTTATTAATAATGATTTAATGATTTAATATTA
1 ATGATTTAATAATAAGGATTTAATGATTTAATACTA
*
75824 ATGATTTAATAATAAGGA-TTAATGATTTGATACTA
1 ATGATTTAATAATAAGGATTTAATGATTTAATACTA
75859 ATGATTTAATAATAA
1 ATGATTTAATAATAA
75874 TTTGATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 30 0.65
36 16 0.35
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.44
Consensus pattern (36 bp):
ATGATTTAATAATAAGGATTTAATGATTTAATACTA
Found at i:75864 original size:21 final size:21
Alignment explanation
Indices: 75800--75864 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
75790 GATTTATTAA
*
75800 TAATGATTTAATGATTTAAT-AT
1 TAATGATTTAAT-A-ATAATGAT
*
75822 TAATGATTTAATAATAAGGAT
1 TAATGATTTAATAATAATGAT
* *
75843 TAATGATTTGATACTAATGAT
1 TAATGATTTAATAATAATGAT
75864 T
1 T
75865 TAATAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.08
21 22 0.59
22 12 0.32
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
TAATGATTTAATAATAATGAT
Found at i:76066 original size:21 final size:21
Alignment explanation
Indices: 76042--76119 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
76032 TATTCAATTC
76042 ATTTAAACAAATAATCTATTA
1 ATTTAAACAAATAATCTATTA
* *
76063 ATTTAAACAAGAATAATATATGA
1 ATTTAAAC-A-AATAATCTATTA
*
76086 A-TT-AACAATTAATCTATTA
1 ATTTAAACAAATAATCTATTA
76105 ATTTAAACAAGATAA
1 ATTTAAACAA-ATAA
76120 CATATGAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 10 0.22
20 3 0.07
21 16 0.35
22 6 0.13
23 11 0.24
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (21 bp):
ATTTAAACAAATAATCTATTA
Found at i:76138 original size:41 final size:42
Alignment explanation
Indices: 76047--76128 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
76037 AATTCATTTA
* *
76047 AACAAATAATCTATTAATTTAAACAAGAATAATATATGAATT
1 AACAATTAATCTATTAATTTAAACAAGAATAACATATGAATT
76089 AACAATTAATCTATTAATTTAAACAAG-ATAACATATGAAT
1 AACAATTAATCTATTAATTTAAACAAGAATAACATATGAAT
76129 AATATATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 12 0.32
42 26 0.68
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.33
Consensus pattern (42 bp):
AACAATTAATCTATTAATTTAAACAAGAATAACATATGAATT
Found at i:76550 original size:24 final size:23
Alignment explanation
Indices: 76522--76600 Score: 97
Period size: 24 Copynumber: 3.4 Consensus size: 23
76512 ATTTGATACA
76522 AATGATTTAGTAATAATTACTAAT
1 AATGATTTA-TAATAATTACTAAT
** *
76546 AATGA-AAATTATAATTACTAAT
1 AATGATTTATAATAATTACTAAT
*
76568 AATGATTTTATAATTATTACTAAT
1 AATGA-TTTATAATAATTACTAAT
76592 AATGATTTA
1 AATGATTTA
76601 ATATGATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 18 0.39
23 5 0.11
24 23 0.50
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (23 bp):
AATGATTTATAATAATTACTAAT
Found at i:76557 original size:57 final size:55
Alignment explanation
Indices: 76440--76561 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 55
76430 ATTAATTATT
** * *
76440 AATTATTAATTTAATGATTTGATATTTAATGATTTTAATGATTACCAATAATATT
1 AATTATTAATTTAATGATTTGATATCAAATGATTTTAATAATTACCAATAATATA
* *
76495 TATTATTATATTTAATGATTTGATA-CAAATGATTTAGTAATAATTACTAATAATGA-A
1 AATTATTA-ATTTAATGATTTGATATCAAATGATTT--TAATAATTACCAATAAT-ATA
76552 AATTA-TAATT
1 AATTATTAATT
76562 ACTAATAATG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
55 18 0.32
56 18 0.32
57 19 0.34
58 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (55 bp):
AATTATTAATTTAATGATTTGATATCAAATGATTTTAATAATTACCAATAATATA
Found at i:76615 original size:24 final size:24
Alignment explanation
Indices: 76522--76616 Score: 70
Period size: 24 Copynumber: 4.0 Consensus size: 24
76512 ATTTGATACA
* * *
76522 AATGATTTAGTAATAATTACTAAT
1 AATGATTTAATAATGATTAATAAT
* * * *
76546 AATGA--AAATTATAATTACTAAT
1 AATGATTTAATAATGATTAATAAT
* * *
76568 AATGATTTTATAATTATTACTAAT
1 AATGATTTAATAATGATTAATAAT
76592 AATGATTTAAT-ATGATTTAATAAT
1 AATGATTTAATAATGA-TTAATAAT
76616 A
1 A
76617 TTAAATAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
22 19 0.33
23 3 0.05
24 36 0.62
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (24 bp):
AATGATTTAATAATGATTAATAAT
Done.