Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002888.1 Hibiscus syriacus cultivar Beakdansim tig00005970_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: 64265
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5812 original size:200 final size:200
Alignment explanation
Indices: 5432--5812 Score: 471
Period size: 200 Copynumber: 1.9 Consensus size: 200
5422 TCCCAGTCTA
* * *
5432 TTACAACATAGCTCAAGGCAAGAATGGTTATCTGTCAACAAAAACTTTCGAGTTTGATTCCATTC
1 TTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTTAATTCCATTC
* * * * * *
5497 AGCTCGATGACATATCAAACGTATGGTAGCAGCGAGAAACTACTTTTCAGTTGAAGCTTAAACTG
66 AGCTCGAGGACATATCAAACATATGGTAGCAGCGAGAAACTACTATCCAGTCGAAGCTTAAACCG
* * * *
5562 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAACAACAAGGAACTATATCCAGT
131 AGGTCTTTAAATCAAGAAGAAGACCAAGGTTGACTACGATTTAACAACAAGGAACTATATCCAGT
5627 CAAAT
196 CAAAT
* *
5632 TTACAACATATCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAAC-TTCGAGTTTAATTCCATTC
1 TTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTTAATTCCATTC
* * * * * * **
5696 AGTTTGAGGGCATATCAACCATATGGTAGCATCGAGGAACTACTATCC-GATCGAATTTTCAAAC
66 AGCTCGAGGACATATCAAACATATGGTAGCAGCGAGAAACTACTATCCAG-TCGAAGCTT-AAAC
* * **
5760 CGATGTCTTTAAAT-AGAGAATAAGACCAAGGTTGACTACGATTTGCCAACAAG
129 CGAGGTCTTTAAATCA-AGAAGAAGACCAAGGTTGACTACGATTTAACAACAAG
5813 AAGCCATATT
Statistics
Matches: 151, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
198 1 0.01
199 63 0.42
200 87 0.58
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (200 bp):
TTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTTAATTCCATTC
AGCTCGAGGACATATCAAACATATGGTAGCAGCGAGAAACTACTATCCAGTCGAAGCTTAAACCG
AGGTCTTTAAATCAAGAAGAAGACCAAGGTTGACTACGATTTAACAACAAGGAACTATATCCAGT
CAAAT
Found at i:6140 original size:2 final size:2
Alignment explanation
Indices: 6124--6156 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
6114 TTTGTATTAT
6124 TA TA TA GTA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
6157 TTCCAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6308 original size:71 final size:71
Alignment explanation
Indices: 6208--6364 Score: 167
Period size: 71 Copynumber: 2.2 Consensus size: 71
6198 TTTGAAAGCG
* ** * ** *** *
6208 TATATAGTTTTTAAAATGTATTTTGAAATATATA-ATATATA-TTTTTGATTTTTTTGAATATAT
1 TATATAGTTTTGAAAACATATTTTGAAATATATATAAATATAGTTTTACAACGTTTTGAAAATAT
6271 ATATATA
66 ATATA-A
6278 TAATATAGTTTTGAAAACAT-TTTTGAAAATATATATAAATATAGTTTTACAACGTTTTGAAAAT
1 T-ATATAGTTTTGAAAACATATTTTG-AAATATATATAAATATAGTTTTACAACGTTTTGAAAAT
6342 ATATATAA
64 ATATATAA
*
6350 TATATAGTTTGGAAA
1 TATATAGTTTTGAAA
6365 TTGTTTTTGA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
70 6 0.08
71 37 0.51
72 8 0.11
73 21 0.29
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (71 bp):
TATATAGTTTTGAAAACATATTTTGAAATATATATAAATATAGTTTTACAACGTTTTGAAAATAT
ATATAA
Found at i:6371 original size:36 final size:36
Alignment explanation
Indices: 6235--6377 Score: 118
Period size: 34 Copynumber: 4.0 Consensus size: 36
6225 GTATTTTGAA
* * * *
6235 ATATATAATATATATTTTTG--ATTTTTTTGAATAT
1 ATATATAATATATAGTTTGGAAATTGTTTTGAAAAT
* *
6269 ATATATATATAATATAGTTTTGAAAACAT-TTTTGAAAAT
1 ATATATA-AT-ATATAG-TTTGGAAA-TTGTTTTGAAAAT
* *
6308 ATATATAA-ATATAGTTT-TACAA-CGTTTTGAAAAT
1 ATATATAATATATAGTTTGGA-AATTGTTTTGAAAAT
6342 ATATATAATATATAGTTTGGAAATTGTTTTTGAAAA
1 ATATATAATATATAGTTTGGAAATTG-TTTTGAAAA
6378 CATTATATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
34 26 0.30
35 18 0.20
36 13 0.15
37 12 0.14
38 1 0.01
39 17 0.19
40 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (36 bp):
ATATATAATATATAGTTTGGAAATTGTTTTGAAAAT
Found at i:6460 original size:11 final size:11
Alignment explanation
Indices: 6444--6475 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
6434 TCATTTTTTA
6444 TATTTATTATT
1 TATTTATTATT
6455 TATTTATT-TT
1 TATTTATTATT
6465 TATTT-TTATT
1 TATTTATTATT
6475 T
1 T
6476 TTTTCAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.10
10 10 0.50
11 8 0.40
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TATTTATTATT
Found at i:8731 original size:28 final size:30
Alignment explanation
Indices: 8695--8763 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
8685 AAATTTTCAC
8695 TTTATTTAAAAAT-AAAATAATTTATAT-T
1 TTTATTTAAAAATAAAAATAATTTATATGT
8723 TTTATTTAAAAATAAAAATAATTTATATGT
1 TTTATTTAAAAATAAAAATAATTTATATGT
*
8753 TTT-TATAAAAA
1 TTTATTTAAAAA
8764 AATATATATG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 13 0.34
29 21 0.55
30 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TTTATTTAAAAATAAAAATAATTTATATGT
Found at i:8765 original size:31 final size:29
Alignment explanation
Indices: 8702--8767 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
8692 CACTTTATTT
**
8702 AAAAAT-AAAATAATTTATATTTTTATTT
1 AAAAATAAAAATAATTTATATTTTTATAA
8730 AAAAATAAAAATAATTTATATGTTTTTATAA
1 AAAAATAAAAATAATTTATA--TTTTTATAA
8761 AAAAATA
1 AAAAATA
8768 TATATGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 6 0.18
29 13 0.39
31 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAAATAAAAATAATTTATATTTTTATAA
Found at i:8787 original size:24 final size:23
Alignment explanation
Indices: 8755--8811 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
8745 TTATATGTTT
8755 TTATAAAAAAATATATATGA-AATAA
1 TTAT-AAAAAATATAT-TGATAAT-A
*
8780 TTATAAAAAATATATTTATAATA
1 TTATAAAAAATATATTGATAATA
8803 TTATAAAAA
1 TTATAAAAA
8812 TATTTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 12 0.40
24 14 0.47
25 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TTATAAAAAATATATTGATAATA
Found at i:8861 original size:19 final size:18
Alignment explanation
Indices: 8839--8892 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
8829 AATAGAATTA
8839 ATTATTTATTTGAAATAAT
1 ATTATTTATTT-AAATAAT
*
8858 ATTA-TT-TTTAAATTAT
1 ATTATTTATTTAAATAAT
8874 A-TATTTAATTTTAAATAAT
1 ATTATTT-A-TTTAAATAAT
8893 TTTAAGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.07
16 9 0.31
17 3 0.10
18 2 0.07
19 13 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTATTTAAATAAT
Found at i:8870 original size:16 final size:17
Alignment explanation
Indices: 8841--8902 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 17
8831 TAGAATTAAT
*
8841 TATTT-ATTTGAAATAA
1 TATTTAATTTTAAATAA
*
8857 TA-TTATTTTTAAATTATA
1 TATTTAATTTTAAA-TA-A
8875 TATTTAATTTTAAATAA
1 TATTTAATTTTAAATAA
*
8892 T-TTTAAGTTTA
1 TATTTAATTTTA
8903 GACTAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.05
16 17 0.45
17 4 0.11
18 5 0.13
19 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTTAATTTTAAATAA
Found at i:9048 original size:23 final size:22
Alignment explanation
Indices: 9003--9085 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
8993 GATAATTTAA
* *
9003 AAATAATATTATGTAAAATAAT
1 AAATAATATTATTTTAAATAAT
*
9025 AATTAATATTATTTTAAATAAAT
1 AAATAATATTATTTTAAAT-AAT
* * *
9048 AAACAATATGATTTTAAAAATAT
1 AAATAATATTATTTTAAATA-AT
*
9071 AAATAAATATAATTT
1 AAAT-AATATTATTT
9086 CATAAATTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.35
23 23 0.47
24 9 0.18
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATAATATTATTTTAAATAAT
Found at i:9858 original size:15 final size:15
Alignment explanation
Indices: 9824--9867 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
9814 ATTTACATTA
9824 AAAATTTTATATAGAATT
1 AAAATTTTA-AT--AATT
*
9842 AATATTTTAATAATT
1 AAAATTTTAATAATT
9857 AAAATTTTAAT
1 AAAATTTTAAT
9868 TTATTAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.58
17 2 0.08
18 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AAAATTTTAATAATT
Found at i:12467 original size:15 final size:16
Alignment explanation
Indices: 12447--12497 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
12437 TGATCGCAAA
12447 TGAATATT-TATTTGT
1 TGAATATTATATTTGT
12462 TGAATATTGA-ATTT-T
1 TGAATATT-ATATTTGT
12477 T--AT-TTATATTTGT
1 TGAATATTATATTTGT
12490 TGAATATT
1 TGAATATT
12498 GGGCTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 13
0.69 0.00 0.31
Matches are distributed among these distances:
11 1 0.03
12 6 0.21
13 4 0.14
15 12 0.41
16 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TGAATATTATATTTGT
Found at i:15646 original size:7 final size:7
Alignment explanation
Indices: 15634--15658 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15624 CCTCCGTACG
15634 CCTTGCA
1 CCTTGCA
15641 CCTTGCA
1 CCTTGCA
15648 CCTTGCA
1 CCTTGCA
15655 CCTT
1 CCTT
15659 TTAGGTGCAC
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:0.12, C:0.44, G:0.12, T:0.32
Consensus pattern (7 bp):
CCTTGCA
Found at i:21026 original size:24 final size:24
Alignment explanation
Indices: 20986--21043 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
20976 CATGGCACTA
* *
20986 CGGTGC-ATTTCTACGTGGTCCTT
1 CGGTGCAAATTCTACGTGGTACTT
21009 CGG-GACAAATTCTACGTGGTACTT
1 CGGTG-CAAATTCTACGTGGTACTT
21033 CGGTGCAAATT
1 CGGTGCAAATT
21044 TATACGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 4 0.13
24 24 0.80
25 1 0.03
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (24 bp):
CGGTGCAAATTCTACGTGGTACTT
Found at i:21591 original size:11 final size:11
Alignment explanation
Indices: 21577--21641 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
21567 GTTTTACGGA
21577 AGTACTGTAGC
1 AGTACTGTAGC
* *
21588 AGTATTGTATC
1 AGTACTGTAGC
*
21599 AGTACTGTAAC
1 AGTACTGTAGC
21610 AGTACTGATA-C
1 AGTACTG-TAGC
* *
21621 AATATTGTAGC
1 AGTACTGTAGC
21632 AGTACTGTAG
1 AGTACTGTAG
21642 TAGGGGAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
10 2 0.05
11 40 0.91
12 2 0.05
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:21602 original size:22 final size:23
Alignment explanation
Indices: 21577--21640 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
21567 GTTTTACGGA
*
21577 AGTACTGTAGCAGTATTGTAT-C
1 AGTACTGTAGCAGTACTGTATAC
*
21599 AGTACTGTAACAGTACTG-ATAC
1 AGTACTGTAGCAGTACTGTATAC
* *
21621 AATATTGTAGCAGTACTGTA
1 AGTACTGTAGCAGTACTGTA
21641 GTAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (23 bp):
AGTACTGTAGCAGTACTGTATAC
Found at i:21614 original size:33 final size:33
Alignment explanation
Indices: 21577--21640 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
21567 GTTTTACGGA
* *
21577 AGTACTG-TAGCAGTATTGTATCAGTACTGTAAC
1 AGTACTGATA-CAATATTGTAGCAGTACTGTAAC
21610 AGTACTGATACAATATTGTAGCAGTACTGTA
1 AGTACTGATACAATATTGTAGCAGTACTGTA
21641 GTAGGGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (33 bp):
AGTACTGATACAATATTGTAGCAGTACTGTAAC
Found at i:21767 original size:19 final size:20
Alignment explanation
Indices: 21724--21770 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
21714 CTGTTCATGG
21724 TACTGTTCATACCGTATAGT
1 TACTGTTCATACCGTATAGT
*
21744 T-CTGTTCATACCGTAT-TT
1 TACTGTTCATACCGTATAGT
21762 TACTGTTCA
1 TACTGTTCA
21771 CAAAATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 22 0.88
20 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (20 bp):
TACTGTTCATACCGTATAGT
Found at i:28786 original size:19 final size:19
Alignment explanation
Indices: 28737--28773 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28727 ACTGTTCATG
*
28737 GTACTATTCATATCATATA
1 GTACTATTCATACCATATA
28756 GTACTATTCATACCATAT
1 GTACTATTCATACCATAT
28774 TTTACTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (19 bp):
GTACTATTCATACCATATA
Found at i:32734 original size:31 final size:31
Alignment explanation
Indices: 32674--32734 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
32664 ATGTATAGGA
*
32674 ATCATCATATATCTAATCAACAATAACATAC
1 ATCATCATATATCTAACCAACAATAACATAC
* * * *
32705 ATCATCATGTATTTAACCAATAATGACATA
1 ATCATCATATATCTAACCAACAATAACATA
32735 TCCCGTTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (31 bp):
ATCATCATATATCTAACCAACAATAACATAC
Found at i:32894 original size:24 final size:24
Alignment explanation
Indices: 32854--32905 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
32844 CAGCTCGCAT
* *
32854 AAATTACATCGAAGTGCCACGTAG
1 AAATTACACCGAAGTGCCACATAG
*
32878 AAATTACACCGAGGTGCCACATAG
1 AAATTACACCGAAGTGCCACATAG
32902 AAAT
1 AAAT
32906 ATCCCAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (24 bp):
AAATTACACCGAAGTGCCACATAG
Found at i:32923 original size:23 final size:23
Alignment explanation
Indices: 32894--32971 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
32884 CACCGAGGTG
*
32894 CCACATAGAAATATCCCAAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* *
32917 CCACATAGTATTGTCCCAAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* * *
32940 CCGCGTAG-AATGTCCCGAAGGA
1 CCACATAGAAATGTCCCAAAGGA
*
32962 CCACGTAGAA
1 CCACATAGAA
32972 CCCTAGACTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.41
23 27 0.59
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (23 bp):
CCACATAGAAATGTCCCAAAGGA
Found at i:32960 original size:22 final size:22
Alignment explanation
Indices: 32907--32971 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
32897 CATAGAAATA
* *
32907 TCCCAAAGGACCACATAGTATTG
1 TCCCAAAGGACCACGTAG-AATG
*
32930 TCCCAAAGGACCGCGTAGAATG
1 TCCCAAAGGACCACGTAGAATG
*
32952 TCCCGAAGGACCACGTAGAA
1 TCCCAAAGGACCACGTAGAA
32972 CCCTAGACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 21 0.57
23 16 0.43
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (22 bp):
TCCCAAAGGACCACGTAGAATG
Found at i:34573 original size:17 final size:17
Alignment explanation
Indices: 34548--34587 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
34538 GTATGTTGTT
*
34548 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
34565 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
34582 CATTTA
1 CATTTA
34588 GGCAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:34666 original size:18 final size:18
Alignment explanation
Indices: 34643--34688 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
34633 ATTCATGCAT
34643 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
34661 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
34679 TTATTTCATT
1 TTAGTTCATT
34689 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:36206 original size:9 final size:8
Alignment explanation
Indices: 36191--36241 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
36181 CCCGGGTTTG
36191 TAAAAAAA
1 TAAAAAAA
36199 TAAAAAAA
1 TAAAAAAA
*
36207 TAAAAAAT
1 TAAAAAAA
*
36215 TCGAAAAAA
1 T-AAAAAAA
*
36224 GAAAAAAA
1 TAAAAAAA
36232 -AAGAAAAA
1 TAA-AAAAA
36240 TA
1 TA
36242 TAAAGGTGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
7 2 0.06
8 27 0.77
9 6 0.17
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:37097 original size:19 final size:19
Alignment explanation
Indices: 37068--37124 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
37058 AAAAAGAAGA
*
37068 AGAAATGAGAGTTGAAAA-
1 AGAATTGAGAGTTGAAAAC
37086 AGACATTGAGAGCATTGAAAAC
1 AGA-ATTGAGAG--TTGAAAAC
37108 AGAATTGAGAG-TGAAAA
1 AGAATTGAGAGTTGAAAA
37125 TGAGCACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 9 0.26
19 7 0.21
21 15 0.44
22 3 0.09
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (19 bp):
AGAATTGAGAGTTGAAAAC
Found at i:39075 original size:17 final size:16
Alignment explanation
Indices: 39044--39077 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
39034 AACGTGAGGA
39044 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
39060 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
39077 T
1 T
39078 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:45456 original size:19 final size:21
Alignment explanation
Indices: 45419--45461 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
45409 TAACTTTTTC
*
45419 TTTTGTCTTTCATTATTAA-T
1 TTTTCTCTTTCATTATTAACT
45439 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
45459 TTT
1 TTT
45462 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:45467 original size:19 final size:20
Alignment explanation
Indices: 45424--45467 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
45414 TTTTCTTTTG
*
45424 TCTTTCATTATTAATTTTTC
1 TCTTTCATTATTAATTTTAC
45444 TCTTTCATT-TTAACTTTTAC
1 TCTTTCATTATTAA-TTTTAC
45464 -CTTT
1 TCTTT
45468 TCTCTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
TCTTTCATTATTAATTTTAC
Found at i:49299 original size:17 final size:16
Alignment explanation
Indices: 49268--49301 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
49258 CACGTGATGA
49268 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
49284 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
49301 T
1 T
49302 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:50159 original size:17 final size:17
Alignment explanation
Indices: 50134--50173 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
50124 GTATGTTATT
*
50134 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
50151 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
50168 CATTTA
1 CATTTA
50174 GGCAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:50200 original size:17 final size:17
Alignment explanation
Indices: 50151--50238 Score: 54
Period size: 17 Copynumber: 5.2 Consensus size: 17
50141 GCATGCATTG
* * *
50151 CATTTAAGCATGTATTT
1 CATTTATGCATCTAGTT
* **
50168 CATTTAGGCAAGTAGTT
1 CATTTATGCATCTAGTT
50185 CATTTATGCATCTAGTT
1 CATTTATGCATCTAGTT
* * *
50202 -ATTTAAT-AAACTACTT
1 CATTT-ATGCATCTAGTT
* *
50218 CATTCATGCATTTAGTT
1 CATTTATGCATCTAGTT
50235 CATT
1 CATT
50239 GAATAAAGTT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
16 12 0.22
17 42 0.78
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (17 bp):
CATTTATGCATCTAGTT
Found at i:50252 original size:18 final size:18
Alignment explanation
Indices: 50229--50274 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
50219 ATTCATGCAT
50229 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
50247 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
50265 TTATTTCATT
1 TTAGTTCATT
50275 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:54939 original size:28 final size:28
Alignment explanation
Indices: 54908--54961 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
54898 AAATTTTATT
* *
54908 TTTTTTAATATTTGTTATTAAGGATGCA
1 TTTTTTAATACTTATTATTAAGGATGCA
*
54936 TTTTTTAATACTTATTATTAGGGATG
1 TTTTTTAATACTTATTATTAAGGATG
54962 GCCATGGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.54
Consensus pattern (28 bp):
TTTTTTAATACTTATTATTAAGGATGCA
Found at i:61208 original size:23 final size:23
Alignment explanation
Indices: 61176--61220 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61166 TAATTCTTTA
*
61176 AAAATCTAAAACATTAAAAAATG
1 AAAATATAAAACATTAAAAAATG
* *
61199 AAAATATAAAATATTAATAAAT
1 AAAATATAAAACATTAAAAAAT
61221 ATAAAAATTA
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:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATATAAAACATTAAAAAATG
Found at i:62968 original size:12 final size:12
Alignment explanation
Indices: 62951--62997 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
62941 CTTAACATTG
62951 TGAAAGAAAAAA
1 TGAAAGAAAAAA
62963 TGAAAGAAAATAA
1 TGAAAGAAAA-AA
*
62976 AGAAA-AAAAAA
1 TGAAAGAAAAAA
62987 TAGAGAAGAAA
1 T-GA-AAGAAA
62998 GAAAAGCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 2 0.07
12 16 0.55
13 8 0.28
14 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (12 bp):
TGAAAGAAAAAA
Found at i:62998 original size:21 final size:21
Alignment explanation
Indices: 62952--63002 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
62942 TTAACATTGT
*
62952 GAAAGAAAAAATGAAAGAAAA
1 GAAAGAAAAAATAAAAGAAAA
* *
62973 TAAAGAAAAAA-AAATAGAGAA
1 GAAAGAAAAAATAAA-AGAAAA
62994 GAAAGAAAA
1 GAAAGAAAA
63003 GCAGAACTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (21 bp):
GAAAGAAAAAATAAAAGAAAA
Found at i:63835 original size:13 final size:13
Alignment explanation
Indices: 63817--63845 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
63807 TTTCCAAGCG
63817 TTTATTTTTTTCT
1 TTTATTTTTTTCT
63830 TTTATTTTTTTCT
1 TTTATTTTTTTCT
63843 TTT
1 TTT
63846 TTGAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTATTTTTTTCT
Done.