Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009143.1 Hibiscus syriacus cultivar Beakdansim tig00112655_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: 45249
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:7796 original size:84 final size:84
Alignment explanation
Indices: 7705--8290 Score: 537
Period size: 84 Copynumber: 7.0 Consensus size: 84
7695 GATTGCCTCT
** * * *
7705 GAGCTGAGTATAGTCGAACTCGAAGGTCTTCGGTTAGCATATAGCCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATG
* *
7770 CTACAAATGATGTGTCTTG
66 CTGCAAATGATGTGCCTTG
** * * * *
7789 GAGCTGAGCGTAGTCGAACTAAAAGGTCTTTTGGTGA-CAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTAT
* * *
7853 ACTGTAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* ** * * * * * *
7874 AAGCTGAGTATAATTGAACTCGAGGGTC-TT--TT-GCAGATAGCCCTTCTCGACTTAAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATG
* *
7935 ATGCAAATAATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * *
7954 GATCTGAGCGTAGTCGAGCTCGGAGGTCTTTGGTTAGCATATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATG
*
8019 CTGCAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * *** *
8038 GAGCTTAGCGTAGTCGAACTCGAAGGTATTTTGGTGA-CAGATAACCCTTCTATCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTAT
* *
8102 GCTGTAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* * * * * * *
8123 AAGCTGAGTGTAATCAAACTTG-AGGTTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTAT
* * *
8183 GCTACAAATGATATGCCTTA
65 GCTGCAAATGATGTGCCTTG
* * * *
8203 GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCATTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATG
* *
8268 CTGCAAATGATATGCATTG
66 CTGCAAATGATGTGCCTTG
8287 GAGC
1 GAGC
8291 CTACCCAATA
Statistics
Matches: 392, Mismatches: 95, Indels: 30
0.76 0.18 0.06
Matches are distributed among these distances:
80 49 0.12
81 73 0.19
83 4 0.01
84 209 0.53
85 57 0.15
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:7963 original size:165 final size:165
Alignment explanation
Indices: 7655--8064 Score: 427
Period size: 165 Copynumber: 2.5 Consensus size: 165
7645 GACCAATTAT
* * * * *
7655 TGACAGATAGCCCTTCTTGCCTTGAGCTATTCTGTAAATTGATTG-CCTCTGAGCTGAGTATAGT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAA-TGATTGCCCTCTGAGCTGAGTATAAT
* * ** *
7719 CGAACTCGAAGGTCTTCGGTTAGCATATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTG
65 CGAACTCGAAGGTCTT--GTTAGCAGATAGCCCTTCTCGACTTAAGCTATAATACAAATAATGTG
*
7784 TCTTGGAGCTGAGCGTAGTCGAACTAAAAGGTCTTTTGG
128 CCTTGGAGCTGAGCGTAGTCGAACTAAAAGGTC-TTTGG
7823 TGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTC-GAAGCTGAGTATAA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGAT-TGCCCTCTG-AGCTGAGTATAA
* * *
7887 TTGAACTCGAGGGTCTT-TT-GCAGATAGCCCTTCTCGACTTAAGCTATAATGCAAATAATGTGC
64 TCGAACTCGAAGGTCTTGTTAGCAGATAGCCCTTCTCGACTTAAGCTATAATACAAATAATGTGC
* * ***
7950 CTTGGATCTGAGCGTAGTCGAGCTCGGAGGTCTTTGG
129 CTTGGAGCTGAGCGTAGTCGAACTAAAAGGTCTTTGG
* * * * * * * * **
7987 TTAGCATATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCT-TGGAGCTTAGCGTA
1 TGA-CAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGAT-TGCCCTCT-GAGCTGAGTATA
*
8050 GTCGAACTCGAAGGT
63 ATCGAACTCGAAGGT
8065 ATTTTGGTGA
Statistics
Matches: 203, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
164 30 0.15
165 100 0.49
166 2 0.01
167 4 0.02
168 37 0.18
169 30 0.15
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATTGCCCTCTGAGCTGAGTATAATC
GAACTCGAAGGTCTTGTTAGCAGATAGCCCTTCTCGACTTAAGCTATAATACAAATAATGTGCCT
TGGAGCTGAGCGTAGTCGAACTAAAAGGTCTTTGG
Found at i:8097 original size:249 final size:249
Alignment explanation
Indices: 7705--8290 Score: 857
Period size: 249 Copynumber: 2.4 Consensus size: 249
7695 GATTGCCTCT
** * *
7705 GAGCTGAGTATAGTCGAACTCGAAGGTCTTCGGTTAGCATATAGCCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTGGTTAGCATATAACCCTTCTCGACTTAAGTTATG
* * * *
7770 CTACAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTAAAAGGTCTTTTGGTGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTAAAAGGTATTTTGGTGACAGATAACC
**
7835 CTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATTGAACTCGAGGG
131 CTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCAAACTCGAGGG
* * * *
7900 TCTTTTGCAGATAGCCCTTCTCGACTTAAGCTATAATGCAAATAATGTGCCTTG
196 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAATACAAATAATATGCCTTA
* * * *
7954 GATCTGAGCGTAGTCGAGCTCGGAGGTCTTTGGTTAGCATATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTGGTTAGCATATAACCCTTCTCGACTTAAGTTATG
* **
8019 CTGCAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTATTTTGGTGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTAAAAGGTATTTTGGTGACAGATAACC
* * * * *
8084 CTTCTATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTTGAGGT
131 CTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCAAACTCGAGGG
* ** *
8149 TCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATATGCCTTA
196 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAATACAAATAATATGCCTTA
* * * *
8203 GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACCATTCTCGACTTAAGTTATG
1 GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTGGTTAGCATATAACCCTTCTCGACTTAAGTTATG
*
8268 CTGCAAATGATATGCATTGGAGC
66 CTGCAAATGATATGCCTTGGAGC
8291 CTACCCAATA
Statistics
Matches: 299, Mismatches: 38, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
249 299 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (249 bp):
GAGCTGAGCCTAGTCGAACTCGAAGGTCTTTGGTTAGCATATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTAAAAGGTATTTTGGTGACAGATAACC
CTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCAAACTCGAGGG
TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAATACAAATAATATGCCTTA
Found at i:11383 original size:23 final size:23
Alignment explanation
Indices: 11357--11400 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11347 AAGGATATTT
* *
11357 CTATGTGGTCCTTCGGGACATAC
1 CTATATGGTCATTCGGGACATAC
11380 CTATATGGTCATTCGGGACAT
1 CTATATGGTCATTCGGGACAT
11401 TCTATGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
CTATATGGTCATTCGGGACATAC
Found at i:14221 original size:20 final size:19
Alignment explanation
Indices: 14180--14231 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
14170 TCTTCATGAG
*
14180 GTATCGATACCGAAGTGGTA
1 GTATCGATACC-AAGTAGTA
*
14200 GTATCGATACCAATGTATTA
1 GTATCGATACCAA-GTAGTA
*
14220 GTATTGATACCA
1 GTATCGATACCA
14232 TTTTTAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (19 bp):
GTATCGATACCAAGTAGTA
Found at i:14731 original size:16 final size:18
Alignment explanation
Indices: 14705--14737 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14695 AGAATAAAAC
14705 ATAAGTTATATG-ATATG
1 ATAAGTTATATGCATATG
14722 ATAA-TTATATGCATAT
1 ATAAGTTATATGCATAT
14738 ATGAAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (18 bp):
ATAAGTTATATGCATATG
Found at i:15175 original size:21 final size:21
Alignment explanation
Indices: 15121--15283 Score: 116
Period size: 21 Copynumber: 7.6 Consensus size: 21
15111 TTGAGGGTTC
*
15121 TATGTGGTCCTTCAGG-ACATA
1 TATGTGGTCCTT-TGGAACATA
**
15142 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
*
15163 TATGTGGTTCTTTGAGACACATA
1 TATGTGGTCCTTTG-GA-ACATA
*
15186 T-T-TGGTCCTTTGGAATATA
1 TATGTGGTCCTTTGGAACATA
* ** * *
15205 TATATGGTCCTTAAGAAGATTTC
1 TATGTGGTCCTTTGGAACA--TA
* *
15228 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTTGGAACATA
* *
15249 TATGTGGTCCTTTGGGATATA
1 TATGTGGTCCTTTGGAACATA
15270 CCTATGTGGTCCTT
1 --TATGTGGTCCTT
15284 CGTGACATAC
Statistics
Matches: 113, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.04
20 5 0.04
21 67 0.59
22 3 0.03
23 33 0.29
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.39
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:15279 original size:23 final size:23
Alignment explanation
Indices: 15227--15302 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
15217 AAGAAGATTT
15227 CTATGTGGTCCTTCGGGACATA-
1 CTATGTGGTCCTTCGGGACATAC
* *
15249 -TATGTGGTCCTTTGGGATATAC
1 CTATGTGGTCCTTCGGGACATAC
*
15271 CTATGTGGTCCTTCGTGACATAC
1 CTATGTGGTCCTTCGGGACATAC
15294 CTATGTGGT
1 CTATGTGGT
15303 TGTTCGATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
21 19 0.40
23 28 0.60
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACATAC
Found at i:16628 original size:23 final size:24
Alignment explanation
Indices: 16593--16637 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
16583 TCGGTCAAAG
* *
16593 TCAACAGTCAACGGGTTGACTCGA
1 TCAACAGTCAACGAGTTAACTCGA
*
16617 TCAA-AGTTAACGAGTTAACTC
1 TCAACAGTCAACGAGTTAACTC
16638 AGTCGAGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (24 bp):
TCAACAGTCAACGAGTTAACTCGA
Found at i:37080 original size:22 final size:22
Alignment explanation
Indices: 37042--37090 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
37032 AGATGATCTT
*
37042 TAAATTATTATTAAAATAAT-A
1 TAAAATATTATTAAAATAATAA
* *
37063 TAAAATATTGATTTAAATTATAA
1 TAAAATATT-ATTAAAATAATAA
37086 TAAAA
1 TAAAA
37091 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
22 9 0.39
23 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TAAAATATTATTAAAATAATAA
Found at i:37083 original size:31 final size:30
Alignment explanation
Indices: 37040--37109 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
37030 TTAGATGATC
* *
37040 TTTAAATTATTATTAAAATAATATAAAATATTGA
1 TTTAAATTA-TAAT-AAA-AATATAAAAAATT-A
37074 TTTAAATTATAATAAAAATATAAAAAATTA
1 TTTAAATTATAATAAAAATATAAAAAATTA
37104 TTTAAA
1 TTTAAA
37110 ACAAATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.21
31 12 0.35
32 3 0.09
33 3 0.09
34 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TTTAAATTATAATAAAAATATAAAAAATTA
Found at i:37539 original size:21 final size:21
Alignment explanation
Indices: 37488--37540 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
37478 ATTATGACTA
37488 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
37509 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
37530 TCGCAATGCGA
1 TCGCAATGCGA
37541 ATAAGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:37555 original size:20 final size:21
Alignment explanation
Indices: 37530--37580 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
37520 TTTTCCCAAT
37530 TCGCAATGCGAA-TAAGAAAA
1 TCGCAATGCGAATTAAGAAAA
* **
37550 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
37571 TCGCAATGCG
1 TCGCAATGCG
37581 GTACTGACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:37594 original size:41 final size:41
Alignment explanation
Indices: 37567--37703 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 41
37557 GCGAATTTGG
* *
37567 AAAATCGCAATGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
37608 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
37648 AATTTCGCAACTCAATACTGACTTTCGCAACGAGAT-ATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
37688 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
37704 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
39 1 0.01
40 40 0.53
41 34 0.45
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:37637 original size:20 final size:20
Alignment explanation
Indices: 37571--37684 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
37561 ATTTGGAAAA
* * *
37571 TCGCAATGCGGTACTGACTA
1 TCGCAACGCGATACTGACTT
* **
37591 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
37612 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
37632 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
* *
37652 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
37672 TCGCAACGAGATA
1 TCGCAACGCGATA
37685 TACATAATCG
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
19 2 0.03
20 56 0.75
21 15 0.20
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:37920 original size:20 final size:21
Alignment explanation
Indices: 37881--37921 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
37871 CCATCTCTGA
37881 CGAAATCCGTCCCCATCTCCAG
1 CGAAATCCGT-CCCATCTCCAG
*
37903 CGAAATCCGT-CTATCTCCA
1 CGAAATCCGTCCCATCTCCA
37922 TCTCTCAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.22
Consensus pattern (21 bp):
CGAAATCCGTCCCATCTCCAG
Found at i:38225 original size:20 final size:20
Alignment explanation
Indices: 38176--38234 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
38166 TTTTATCTCT
* **
38176 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
38196 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
38216 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
38235 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:38423 original size:25 final size:24
Alignment explanation
Indices: 38369--38423 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
38359 ATGTTATTAT
* *
38369 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
38393 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
38419 TGTTT
1 TGTTT
38424 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:39556 original size:18 final size:18
Alignment explanation
Indices: 39535--39582 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
39525 TCCACTTCGG
39535 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
39553 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
39571 GAGCCATCACCT
1 GAGCCATCACCT
39583 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:40149 original size:19 final size:20
Alignment explanation
Indices: 40095--40161 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
40085 TAGTTTACTT
* *
40095 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
40115 TTGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
40135 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
40154 TCGCAACG
1 TCGCAACG
40162 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:40473 original size:20 final size:20
Alignment explanation
Indices: 40448--40497 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
40438 CACGAAACTT
40448 AACGCGAAAAT-GACTATCGC
1 AACGCGAAAATAG-CTATCGC
*
40468 AACGCGGAAATAGCTATCGC
1 AACGCGAAAATAGCTATCGC
*
40488 AATGCGAAAA
1 AACGCGAAAA
40498 AATCGCAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (20 bp):
AACGCGAAAATAGCTATCGC
Found at i:40534 original size:19 final size:19
Alignment explanation
Indices: 40510--40569 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
40500 TCGCAACGAC
*
40510 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
40529 AAAATCGCAACGCGAAA-C
1 AAAATCGCAACGCGAAATG
40547 ACAAATCGCAACGCGAAATG
1 A-AAATCGCAACGCGAAATG
40567 AAA
1 AAA
40570 CCGCAGTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 34 0.94
20 1 0.03
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:40553 original size:38 final size:33
Alignment explanation
Indices: 40483--40569 Score: 99
Period size: 38 Copynumber: 2.6 Consensus size: 33
40473 GGAAATAGCT
40483 ATCGCAATGCG-AA--AAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
40513 ATCGCAATGCGAAATGAAAATCGCAACGCGAAACACAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--ACA-AA
*
40551 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40570 CCGCAGTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
30 11 0.23
31 2 0.04
33 10 0.21
35 2 0.04
37 3 0.06
38 20 0.42
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:41779 original size:14 final size:14
Alignment explanation
Indices: 41760--41795 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41750 ATTGTTTAAT
41760 TGATTTGTAAAAAA
1 TGATTTGTAAAAAA
* *
41774 TGATTTGTAAATAT
1 TGATTTGTAAAAAA
41788 TGATTTGT
1 TGATTTGT
41796 TTATTTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAAA
Found at i:41955 original size:18 final size:18
Alignment explanation
Indices: 41932--41995 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 18
41922 TCGCAACGAG
41932 AATCGCAATGCGAATGAA
1 AATCGCAATGCGAATGAA
*
41950 AATCGCAATGCGAAATAAA
1 AATCGCAATGCG-AATGAA
41969 AATCGCAA--CG-A-GAA
1 AATCGCAATGCGAATGAA
41983 AATCGCAATGCGA
1 AATCGCAATGCGA
41996 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 12 0.30
19 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (18 bp):
AATCGCAATGCGAATGAA
Found at i:42045 original size:20 final size:20
Alignment explanation
Indices: 42022--42109 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
42012 CGATTTCTAA
42022 GTTGCGATAGCCATTTTCAC
1 GTTGCGATAGCCATTTTCAC
***
42042 GTTGCGATTTTTCA-TTTCGA-
1 GTTGCGA-TAGCCATTTTC-AC
* *
42062 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCAC
**
42082 GTTGCGATAGCCATTTTCGT
1 GTTGCGATAGCCATTTTCAC
42102 GTTGCGAT
1 GTTGCGAT
42110 TTCCCCGTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.06
20 47 0.87
21 4 0.07
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCAC
Found at i:42107 original size:40 final size:40
Alignment explanation
Indices: 42021--42109 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
42011 GCGATTTCTA
***
42021 AGTTGCGATAGCCATTTTCACGTTGCGATTTTTCATTTCG
1 AGTTGCGATAGCCATTTTCACGTTGCGATTAGCCATTTCG
* *
42061 AATTGCGATAGCCATTTTCGCGTTGCGA-TAGCCATTTTCG
1 AGTTGCGATAGCCATTTTCACGTTGCGATTAGCCA-TTTCG
*
42101 TGTTGCGAT
1 AGTTGCGAT
42110 TTCCCCGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.07
40 38 0.93
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (40 bp):
AGTTGCGATAGCCATTTTCACGTTGCGATTAGCCATTTCG
Found at i:42347 original size:20 final size:20
Alignment explanation
Indices: 42322--42371 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
42312 TTGAAGATGA
42322 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
42342 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
42362 TTGCGATTTT
1 TTGCGATTTT
42372 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:43783 original size:14 final size:14
Alignment explanation
Indices: 43749--43787 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
43739 TTGATTGTTT
43749 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
43763 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
43777 TGTTGATTTGT
1 AATTGATTTGT
43788 TTATTTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:43939 original size:19 final size:19
Alignment explanation
Indices: 43915--43963 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
43905 ATCGCAACGA
43915 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
43934 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
43953 AAAAATCGCAA
1 GAAAATCGCAA
43964 CGAGAAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:44312 original size:21 final size:21
Alignment explanation
Indices: 44286--44353 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
44276 TTGAAGATGA
44286 TTGCGATTTTTCAGAATCTCG
1 TTGCGATTTTTCAGAATCTCG
**
44307 TTGCGA--AGTCAGAATCTCG
1 TTGCGATTTTTCAGAATCTCG
**
44326 TTGCGATTTTGT-ATTATCTCG
1 TTGCGATTTT-TCAGAATCTCG
44347 TTGCGAT
1 TTGCGAT
44354 AGTCAGTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 17 0.45
21 20 0.53
22 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTTCAGAATCTCG
Done.