Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003920.1 Hibiscus syriacus cultivar Beakdansim tig00008473_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: 69860
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:8058 original size:30 final size:30
Alignment explanation
Indices: 7987--8069 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
7977 CCCGAAGGAC
* * *
7987 CTATTCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
8016 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* * *
8046 CTGTCCATAGGTCCCAAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
8070 AGGTAAACTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:8098 original size:31 final size:31
Alignment explanation
Indices: 8044--8139 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
8034 GAACCTCGGC
** * * *
8044 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATATTCCATAGAACATAGGTA
* *
8075 AACTGTTCATATATTCCTTAGAACATAGGTA
1 AACTGTCCATATATTCCATAGAACATAGGTA
* *
8106 TACTGTCCATATGTTCCATAGAACATAGGTA
1 AACTGTCCATATATTCCATAGAACATAGGTA
8137 AAC
1 AAC
8140 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATATTCCATAGAACATAGGTA
Found at i:8868 original size:24 final size:20
Alignment explanation
Indices: 8819--8876 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
8809 TTCCCATTGA
*
8819 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
8839 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
8862 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
8877 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:12470 original size:24 final size:23
Alignment explanation
Indices: 12414--12474 Score: 104
Period size: 23 Copynumber: 2.6 Consensus size: 23
12404 TTCCCATTGA
*
12414 AGTGCATCGGTGCATTCTTTAAC
1 AGTGCATCGATGCATTCTTTAAC
12437 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTCTTTAAC
12460 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
12475 CTACCATGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (23 bp):
AGTGCATCGATGCATTCTTTAAC
Found at i:13701 original size:20 final size:20
Alignment explanation
Indices: 13673--13713 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13663 CGACAAATGT
* *
13673 TAAAGGACAGGGAATATCTC
1 TAAAAGACAGGGAATACCTC
*
13693 TAAAAGACATGGAATACCTC
1 TAAAAGACAGGGAATACCTC
13713 T
1 T
13714 GTAAAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (20 bp):
TAAAAGACAGGGAATACCTC
Found at i:19533 original size:44 final size:44
Alignment explanation
Indices: 19480--19589 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
19470 GAGGTTTAAA
* *
19480 TCCATCACATAAGGAGTTGGATCAACATTACCACTTCGATCGAT
1 TCCATCACATAAGGAGTTGGATCAACATCACCACTTCCATCGAT
* * * * * *
19524 TCTATCACATAAGGAGTTAGATCATCATCATCATTTCCTTCGAT
1 TCCATCACATAAGGAGTTGGATCAACATCACCACTTCCATCGAT
19568 TCCATCACATAAGGAGTTGGAT
1 TCCATCACATAAGGAGTTGGAT
19590 TAGTATGTTC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATCAACATCACCACTTCCATCGAT
Found at i:19706 original size:179 final size:181
Alignment explanation
Indices: 19385--19735 Score: 492
Period size: 179 Copynumber: 1.9 Consensus size: 181
19375 ACCTTCGTTT
* * * *
19385 GATTCTATCACATAAGGAGTTGGATCAACATCATCTCGCTCGAGATAGTTTCCCTTTAAACTCAG
1 GATTCCATCACATAAGGAGTTGGATCAACATCATCTCGCTCAAGATAGTTTCCCTTGAAACTCAA
* * * *
19450 ACTTTAGTATCATTTCACTTGAGGTTTAAATCCATCACATAAGGAGTTGGATCAACATTACCACT
66 ACTTCAGTATCATTTCACTTGAGGTCTAAATCAATCACATAAGGAGTTGAATCAACATTACCACT
*
19515 TCGATCGATTC-TATCACATAAGGAGTTAGATCATCATCATCATTTCCTTC
131 TCGATCGATTCATATCACATAAGGAGTTAGATCAGCATCATCATTTCCTTC
* ** **
19565 GATTCCATCACATAAGGAGTTGGATTAGTATGTTCTCGCTCAAGATAGTTT-CCTTGAAACTCAA
1 GATTCCATCACATAAGGAGTTGGATCAACATCATCTCGCTCAAGATAGTTTCCCTTGAAACTCAA
* * *
19629 ACTTCAGTATCATTTCACTTGATGTCTAAATCAATCACATAAGGAGTTGAATCATCATTATCACT
66 ACTTCAGTATCATTTCACTTGAGGTCTAAATCAATCACATAAGGAGTTGAATCAACATTACCACT
* *
19694 TC-ACTTGATTCTATATCACATAAGGAGTTGGATCAGCATCAT
131 TCGA-TCGATTC-ATATCACATAAGGAGTTAGATCAGCATCAT
19736 TTCATAGAGA
Statistics
Matches: 149, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
178 1 0.01
179 77 0.52
180 44 0.30
181 27 0.18
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (181 bp):
GATTCCATCACATAAGGAGTTGGATCAACATCATCTCGCTCAAGATAGTTTCCCTTGAAACTCAA
ACTTCAGTATCATTTCACTTGAGGTCTAAATCAATCACATAAGGAGTTGAATCAACATTACCACT
TCGATCGATTCATATCACATAAGGAGTTAGATCAGCATCATCATTTCCTTC
Found at i:21986 original size:2 final size:2
Alignment explanation
Indices: 21979--22032 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
21969 CTAATAATAC
21979 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
22021 AT AT AT AT AT AT
1 AT AT AT AT AT AT
22033 GAAATTTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22580 original size:39 final size:39
Alignment explanation
Indices: 22526--22641 Score: 153
Period size: 38 Copynumber: 3.0 Consensus size: 39
22516 AAAATCATGA
*
22526 GGTAAGAATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
1 GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
* * * *
22565 GGTAAGGACTTACCCTGT-GCAAAAGTAGAGGAGCTTGT
1 GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
* * *
22603 AGTAAGGATTTACCCTGTGCAAAAAATAGAGGAGCCTGC
1 GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
22642 AGCAAGGTCT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 33 0.52
39 31 0.48
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (39 bp):
GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
Found at i:26362 original size:14 final size:14
Alignment explanation
Indices: 26343--26372 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
26333 ACCTTGAATT
26343 CAACCTTATTTCTG
1 CAACCTTATTTCTG
26357 CAACCTTATTTCTG
1 CAACCTTATTTCTG
26371 CA
1 CA
26373 TTGATTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (14 bp):
CAACCTTATTTCTG
Found at i:32379 original size:27 final size:27
Alignment explanation
Indices: 32340--32399 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
32330 GAAAATAATG
32340 TAAC-AAAGAAAAGGAAAAGAAAAAAAA
1 TAACAAAAGAAAAGGAAAA-AAAAAAAA
* *
32367 TAACAAAAG-AAAGTAAAAAAAACAAA
1 TAACAAAAGAAAAGGAAAAAAAAAAAA
32393 -AACAAAA
1 TAACAAAA
32400 AATCATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.23
26 7 0.23
27 12 0.40
28 4 0.13
ACGTcount: A:0.78, C:0.07, G:0.10, T:0.05
Consensus pattern (27 bp):
TAACAAAAGAAAAGGAAAAAAAAAAAA
Found at i:32424 original size:17 final size:17
Alignment explanation
Indices: 32381--32430 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
32371 AAAAGAAAGT
*
32381 AAAAAAA-ACAAA-AAC
1 AAAAAAATAAAAATAAC
32396 AAAAAATCATAAAAATAAC
1 AAAAAA--ATAAAAATAAC
*
32415 AAAAAAATAATAATAA
1 AAAAAAATAAAAATAA
32431 TATGTAGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 6 0.21
17 10 0.34
18 4 0.14
19 9 0.31
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAAAATAAC
Found at i:34862 original size:73 final size:73
Alignment explanation
Indices: 34738--34878 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 73
34728 TTTTAAATTT
* * * **
34738 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTTAAATACTTGAAAATATGGTAATTTAG
1 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCGAAAATATAATAATTTAG
34803 TGGGCTTC
66 TGGGCTTC
34811 AATAATTAAAAAATATTTTTAAACATCA-TTTTTTATTTAAAAAACTCGAAAATATAATAATTTA
1 AATAATTAAAAAATATTTTTAAACAT-ATTTTTTTATTTAAAAAACTCGAAAATATAATAATTTA
34875 GTGG
65 GTGG
34879 AGCCCCATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 61 0.98
74 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (73 bp):
AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCGAAAATATAATAATTTAG
TGGGCTTC
Found at i:48469 original size:30 final size:31
Alignment explanation
Indices: 48433--48496 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
48423 GGAATGCTTT
*
48433 TGCTTGA-TTTTTGTTATGTAAATTAGAAAA
1 TGCTTGATTTTTTGTTATGTAAATCAGAAAA
*
48463 TGCTTGATTTTTTTTTTATGTAAATCAGAAAA
1 TGCTTGA-TTTTTTGTTATGTAAATCAGAAAA
48495 TG
1 TG
48497 GAAATGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 7 0.23
32 23 0.77
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (31 bp):
TGCTTGATTTTTTGTTATGTAAATCAGAAAA
Found at i:54050 original size:59 final size:60
Alignment explanation
Indices: 53974--54150 Score: 202
Period size: 59 Copynumber: 3.0 Consensus size: 60
53964 CACAAATGAT
53974 CCCCAA-CTATAGTATAATGTTTTATT-AGGTCTCTTGACTATTAAAAGTTATAAAATGGT-
1 CCCCAATC-ATAGTATAATGTTTTATTGA-GTCTCTTGACTATTAAAAGTTATAAAATGGTC
* * * * *
54033 CCCTAATCATAGTATAATGCTTTATTGAATCTCTTGACTATTAAACGTTACAAAATGGTC
1 CCCCAATCATAGTATAATGTTTTATTGAGTCTCTTGACTATTAAAAGTTATAAAATGGTC
* * * *
54093 CCCCGATCATAGGA-AGTTGTTTTGTTGAGTCT-TTCGACTATTAAAAGTTATAAAATGG
1 CCCCAATCATAGTATA-ATGTTTTATTGAGTCTCTT-GACTATTAAAAGTTATAAAATGG
54151 CCACTCAACT
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
59 53 0.54
60 46 0.46
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (60 bp):
CCCCAATCATAGTATAATGTTTTATTGAGTCTCTTGACTATTAAAAGTTATAAAATGGTC
Found at i:56972 original size:3 final size:3
Alignment explanation
Indices: 56964--57005 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
56954 GAGATATGAG
*
56964 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
57006 TAAAAAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:57775 original size:34 final size:32
Alignment explanation
Indices: 57713--57782 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
57703 ACCTTACAAC
* *
57713 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
* *
57745 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
57779 TCCC
1 TCCC
57783 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:58233 original size:20 final size:19
Alignment explanation
Indices: 58147--58237 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
58137 ATTGCAGCCT
* *
58147 TGATGCATGGATGCATGGCA
1 TGATGCATCGATGCATTG-A
* *
58167 GGATGCATCGATGCACT-A
1 TGATGCATCGATGCATTGA
* *
58185 AG-TGCATTCGATG-TTTGA
1 TGATGCA-TCGATGCATTGA
*
58203 -G-TGCATGGATGCATTGCA
1 TGATGCATCGATGCATTG-A
58221 TGATGCATCGATGCATT
1 TGATGCATCGATGCATT
58238 AGTGCAGGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
16 5 0.09
17 13 0.24
18 10 0.18
19 1 0.02
20 26 0.47
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
TGATGCATCGATGCATTGA
Found at i:58272 original size:21 final size:20
Alignment explanation
Indices: 58204--58301 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 20
58194 GATGTTTGAG
* *
58204 TGCATGGATGCATTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
58224 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
58246 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
* *
58267 TGCATGGATTCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGA
*
58288 TGCATGAATGCACT
1 TGCATGGATGCACT
58302 TTGACACCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.08
20 12 0.19
21 31 0.48
22 10 0.16
23 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:58402 original size:29 final size:29
Alignment explanation
Indices: 58381--58438 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
58371 AAACTTTGAA
58381 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
58410 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
58439 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:58428 original size:30 final size:30
Alignment explanation
Indices: 58381--58440 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
58371 AAACTTTGAA
58381 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
58410 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
58441 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:61527 original size:20 final size:22
Alignment explanation
Indices: 61502--61541 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
61492 TGTTGTATAT
61502 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
61522 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
61542 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:61597 original size:21 final size:21
Alignment explanation
Indices: 61571--61619 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
61561 CATAACATGA
61571 TGCATCGGTGCACTATCAAGT
1 TGCATCGGTGCACTATCAAGT
61592 TGCATCGGTGCACTATCAAGT
1 TGCATCGGTGCACTATCAAGT
61613 TGCATCG
1 TGCATCG
61620 ATACCCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGGTGCACTATCAAGT
Found at i:61715 original size:20 final size:20
Alignment explanation
Indices: 61692--61738 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
61682 ATTCATGGCA
61692 CGATGCATGGCAGAATGCAT
1 CGATGCATGGCAGAATGCAT
*
61712 CGATGCATGGCAGGATGCAT
1 CGATGCATGGCAGAATGCAT
61732 CGATGCA
1 CGATGCA
61739 CTAAGTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (20 bp):
CGATGCATGGCAGAATGCAT
Found at i:61829 original size:21 final size:21
Alignment explanation
Indices: 61803--61858 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
61793 TTAGTGCAGG
*
61803 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGA
*
61824 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTACAGGGA
61845 TGCATGGATGCACT
1 TGCATGGATGCACT
61859 TTGACACCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:61959 original size:29 final size:29
Alignment explanation
Indices: 61938--61995 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
61928 AAACTTTGAA
61938 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
61967 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
61996 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:61985 original size:30 final size:30
Alignment explanation
Indices: 61938--61997 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
61928 AAACTTTGAA
61938 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
61967 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
61998 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:62203 original size:45 final size:45
Alignment explanation
Indices: 62152--62248 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 45
62142 GTTAAGCTCT
62152 CCCTTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
1 CCCTTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
* *
62197 CCC-TTTTTCATTAAGAAATTGAATTTTTCAAACCAAACTTCTCC
1 CCCTTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
62241 CCCTTTTT
1 CCCTTTTT
62249 GTTATATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 42 0.86
45 7 0.14
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (45 bp):
CCCTTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
Found at i:63864 original size:15 final size:16
Alignment explanation
Indices: 63846--63875 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63836 TTCTTCTTGT
63846 TTTTCTTC-TCTTCCC
1 TTTTCTTCATCTTCCC
63861 TTTTCTTCATCTTCC
1 TTTTCTTCATCTTCC
63876 TTCATCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTCTTCATCTTCCC
Found at i:65416 original size:21 final size:20
Alignment explanation
Indices: 65348--65445 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 20
65338 GATGTTTGAG
* *
65348 TGCATGGATGCATTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
65368 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
65390 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
* *
65411 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTGCA-GGA
65432 TGCATGGATGCACT
1 TGCATGGATGCACT
65446 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.08
20 12 0.18
21 33 0.50
22 10 0.15
23 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:65434 original size:42 final size:42
Alignment explanation
Indices: 65347--65445 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
65337 CGATGTTTGA
* * * **
65347 GTGCATGGATGCATTGCATGATGCATCGATGCATTAGTGCAG
1 GTGCATGGATGCACTGCAGGATGCATCGATGCACTACAGCAG
* *
65389 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTACAG-GG
1 GTGCATGGATGCACTGCA-GGATGCATCGATGCACTACAGCAG
65431 GTGCATGGATGCACT
1 GTGCATGGATGCACT
65446 TTGACACCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 33 0.67
43 16 0.33
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGATGCATCGATGCACTACAGCAG
Found at i:65546 original size:29 final size:30
Alignment explanation
Indices: 65514--65581 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
65504 GAAACCTTTT
65514 AAAACATTGAATAAATTCAATT-AAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
***
65543 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
65573 AAAATCATT
1 AAAA-CATT
65582 TTGCCTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 19 0.56
30 11 0.32
31 4 0.12
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAACATTGAATAAATTCAATTCAAGTCCA
Found at i:65572 original size:30 final size:30
Alignment explanation
Indices: 65525--65584 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
65515 AAACATTGAA
65525 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
65554 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
65585 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:66343 original size:3 final size:3
Alignment explanation
Indices: 66335--66436 Score: 154
Period size: 3 Copynumber: 33.7 Consensus size: 3
66325 GTTTTGTTTG
66335 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
66382 TAA TAA TAA TAA TAA T-A TAAA TAA TAA TAA TAA TTAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA
66428 TAAA TAA TA
1 T-AA TAA TA
66437 TATATATAGC
Statistics
Matches: 92, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
2 4 0.04
3 80 0.87
4 8 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Done.