Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005973.1 Hibiscus syriacus cultivar Beakdansim tig00014042_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: 66388
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:348 original size:21 final size:20
Alignment explanation
Indices: 258--353 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
248 GATGCACCTA
* *
258 TCATCATTCAAGAGG-CGCT
1 TCATCGTTCAAGAGGCCCCT
*
277 TCTATCGTTCAAGAGGGCCCT
1 TC-ATCGTTCAAGAGGCCCCT
* *
298 CTCATC-ATCGAAGAAGCCCC-
1 -TCATCGTTC-AAGAGGCCCCT
**
318 TCCCCGTTCAAGAGGCCCCT
1 TCATCGTTCAAGAGGCCCCT
338 GTCATCGTTCAAGAGG
1 -TCATCGTTCAAGAGG
354 TCCTGCCCGC
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
19 14 0.24
20 16 0.27
21 27 0.46
22 2 0.03
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:2177 original size:37 final size:38
Alignment explanation
Indices: 2129--2209 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
2119 AGTTATAGAT
*
2129 TTTGATTTCC-TTTGCTTGGCACCATATGAGATTTGGA
1 TTTGATTTCCTTTTGCTTGACACCATATGAGATTTGGA
* *
2166 TTTGATTTCCTTTTGCTTGACACTATATGAGCTTTGGA
1 TTTGATTTCCTTTTGCTTGACACCATATGAGATTTGGA
2204 TTTGAT
1 TTTGAT
2210 GAGTATCGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 10 0.25
38 30 0.75
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.47
Consensus pattern (38 bp):
TTTGATTTCCTTTTGCTTGACACCATATGAGATTTGGA
Found at i:2971 original size:25 final size:25
Alignment explanation
Indices: 2937--2986 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2927 ATTATTTTTC
*
2937 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2962 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2987 TAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:3118 original size:20 final size:20
Alignment explanation
Indices: 3087--3196 Score: 139
Period size: 20 Copynumber: 5.5 Consensus size: 20
3077 CGGTTTGCGA
*
3087 TTTCGGGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
3107 TATCGCGTTGCGAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
* *
3127 TTTCGCGTTGCAAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
*
3147 TTTCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
3167 TTTCGTGTTGTGAAGTTGAC
1 TTTCGCGTTGCGAATTTGAC
3187 TTTCGCGTTG
1 TTTCGCGTTG
3197 ATCGCAACAT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:3502 original size:18 final size:17
Alignment explanation
Indices: 3479--3518 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
3469 AAGCCGGTTG
*
3479 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGA-TT
3497 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
3514 TGATT
1 TGATT
3519 TCCTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.55
Consensus pattern (17 bp):
TGATTGCGATTTTGATT
Found at i:5777 original size:24 final size:24
Alignment explanation
Indices: 5743--5796 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5733 CTATCACATC
5743 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* * *
5767 ATCAAAGTCTGGGTATTGACCAGG
1 ATCAAAATCTGAGTATTGACCAAG
5791 ATCAAA
1 ATCAAA
5797 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:5943 original size:12 final size:12
Alignment explanation
Indices: 5922--5955 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5912 GGTTGTGGGT
*
5922 TTTGAGATTGTG
1 TTTGATATTGTG
5934 TTTGATATTGTG
1 TTTGATATTGTG
*
5946 TTTGGTATTG
1 TTTGATATTG
5956 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:6873 original size:3 final size:3
Alignment explanation
Indices: 6865--6890 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6855 GAATTGAGTT
6865 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
6891 TGGAAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:12618 original size:14 final size:14
Alignment explanation
Indices: 12599--12628 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12589 ATATAACATT
*
12599 TTACGAAAATTGAG
1 TTACGAAAATCGAG
12613 TTACGAAAATCGAG
1 TTACGAAAATCGAG
12627 TT
1 TT
12629 GCATTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (14 bp):
TTACGAAAATCGAG
Found at i:20821 original size:8 final size:7
Alignment explanation
Indices: 20808--20959 Score: 54
Period size: 7 Copynumber: 21.4 Consensus size: 7
20798 TATGCATACA
20808 ATATAAGT
1 ATATAA-T
20816 ATATAAT
1 ATATAAT
20823 ATA-AAT
1 ATATAAT
*
20829 ATA-CAT
1 ATATAAT
*
20835 -TATACT
1 ATATAAT
20841 -TATAAT
1 ATATAAT
*
20847 ATAT-GT
1 ATATAAT
*
20853 ATACAAT
1 ATATAAT
*
20860 GTAT-AT
1 ATATAAT
20866 ATA-AAGT
1 ATATAA-T
20873 ATATAAATT
1 ATAT-AA-T
20882 ATATAGCAT
1 ATATA--AT
20891 A-AGTATAT
1 ATA-TA-AT
20899 ATATAAT
1 ATATAAT
*
20906 ATACAAT
1 ATATAAT
*
20913 -TA-CAT
1 ATATAAT
20918 ATATAAGT
1 ATATAA-T
20926 ATATAAT
1 ATATAAT
*
20933 ATATAAGA
1 ATATAA-T
20941 ATATAAACT
1 ATAT-AA-T
20950 ATATAAT
1 ATATAAT
20957 ATA
1 ATA
20960 AGCATATATA
Statistics
Matches: 110, Mismatches: 18, Indels: 33
0.68 0.11 0.20
Matches are distributed among these distances:
5 4 0.04
6 27 0.25
7 34 0.31
8 26 0.24
9 18 0.16
10 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (7 bp):
ATATAAT
Found at i:20848 original size:37 final size:37
Alignment explanation
Indices: 20807--20935 Score: 99
Period size: 37 Copynumber: 3.5 Consensus size: 37
20797 TTATGCATAC
20807 AATATAAGTATATAATATAAATATACATTATACTTAT
1 AATATAAGTATATAATATAAATATACATTATACTTAT
* * * * * *
20844 AATATATGTATACAATGTATATATAAAGTATATAAATTAT
1 AATATAAGTATATAATATAAATATACA-T-TAT-ACTTAT
* *
20884 ATAGCATAAGTATAT-ATAT-AATATACAAT-TAC--AT
1 A-A-TATAAGTATATAATATAAATATACATTATACTTAT
20918 -ATATAAGTATATAATATA
1 AATATAAGTATATAATATA
20936 TAAGAATATA
Statistics
Matches: 70, Mismatches: 15, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
31 10 0.14
32 5 0.07
34 2 0.03
36 1 0.01
37 23 0.33
38 2 0.03
39 3 0.04
40 12 0.17
41 4 0.06
42 8 0.11
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (37 bp):
AATATAAGTATATAATATAAATATACATTATACTTAT
Found at i:20868 original size:24 final size:22
Alignment explanation
Indices: 20815--20869 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
20805 ACAATATAAG
20815 TATATAATATAAATATACATTA
1 TATATAATATAAATATACATTA
**
20837 TACTTATAATATATGTATACAATGTA
1 TA--TATAATATAAATATAC-AT-TA
20863 TATATAA
1 TATATAA
20870 AGTATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
24 19 0.70
25 2 0.07
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (22 bp):
TATATAATATAAATATACATTA
Found at i:20908 original size:31 final size:28
Alignment explanation
Indices: 20863--20938 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 28
20853 ATACAATGTA
*
20863 TATATAAAGTATATAAATTATATAGCATAAG
1 TATAT-AA-TATATAAATTACATA-CATAAG
*
20894 TATATATATAATATACAATTACATATATAAG
1 TATATA-AT-ATATA-AATTACATACATAAG
20925 TATATAATATATAA
1 TATATAATATATAA
20939 GAATATAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 1 0.03
29 5 0.12
30 4 0.10
31 22 0.55
32 8 0.20
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (28 bp):
TATATAATATATAAATTACATACATAAG
Found at i:20936 original size:15 final size:16
Alignment explanation
Indices: 20916--20959 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
20906 ATACAATTAC
20916 ATATATAAGTATAT-A
1 ATATATAAGTATATAA
*
20931 ATATATAAGAATATAA
1 ATATATAAGTATATAA
20947 ACTATATAA-TATA
1 A-TATATAAGTATA
20960 AGCATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (16 bp):
ATATATAAGTATATAA
Found at i:20983 original size:2 final size:2
Alignment explanation
Indices: 20978--21009 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20968 TACAAGTGTG
20978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21010 ATTGTAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21576 original size:2 final size:2
Alignment explanation
Indices: 21571--21843 Score: 199
Period size: 2 Copynumber: 138.0 Consensus size: 2
21561 GAAAAAATAC
21571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
21613 CT- TA TG CA TA TG TA TA CT- TA TA TA TA TA AA AA GTG TG TG TG
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* *
21654 TA TA TA TA TA TA TA TA TA TA TA TA AA GTA TA GA -A TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * * *
21695 GTA TA TT TA TA -A GTA TA CA -A TA TA TG CA TA -A GA -A TG TA TA
1 -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
21735 TA TA CA TA TA TG TA -A GTA TA TA -A TG TGA TG TA TG TA TA TA -A
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA TA TA
21776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21818 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
21844 ATTAAACATG
Statistics
Matches: 220, Mismatches: 32, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
1 11 0.05
2 202 0.92
3 7 0.03
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:22187 original size:43 final size:43
Alignment explanation
Indices: 22136--22221 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
22126 AAATTCTATA
* * *
22136 TTCCCTCTAAATTTCCAATTTCACTTTATTCCCAAAAATTTCC
1 TTCCCTCTAAATTCCCAAATTCACTCTATTCCCAAAAATTTCC
* * *
22179 TTCCCTCTAAATTCCCAAATTCTCTCTATTCTCAAAATTTTCC
1 TTCCCTCTAAATTCCCAAATTCACTCTATTCCCAAAAATTTCC
22222 AATTTTCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (43 bp):
TTCCCTCTAAATTCCCAAATTCACTCTATTCCCAAAAATTTCC
Found at i:23807 original size:17 final size:17
Alignment explanation
Indices: 23772--23817 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
23762 CTAAACAAAT
* *
23772 AAATAAAAATAACGGTA
1 AAATAAAAAAAACGCTA
*
23789 AAATAAAAAAAATGCTA
1 AAATAAAAAAAACGCTA
*
23806 AAACAAAAAAAA
1 AAATAAAAAAAA
23818 AGGTATGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.13
Consensus pattern (17 bp):
AAATAAAAAAAACGCTA
Found at i:27710 original size:43 final size:42
Alignment explanation
Indices: 27649--27848 Score: 104
Period size: 43 Copynumber: 4.7 Consensus size: 42
27639 AGCTCCTGTT
** *
27649 TTTTTCAATATTACTTTTTACCTTTATAATTGAGGCCACAAAA
1 TTTTTCAATCCTATTTTTTACCTTTATAATTGAGGCC-CAAAA
* * **
27692 TTTTTCAATCCTATTTTTTA-CTCATATAATTTAGGCCCCAATTTT
1 TTTTTCAATCCTATTTTTTACCT-TTATAATTGAGG-CCCAA--AA
** * * **
27737 TTTTTCAATCTCGCTTTTTTACCTTTAAAATTGATGCCCATATT
1 TTTTTCAATC-CTATTTTTTACCTTTATAATTGAGGCCCA-AAA
** * *
27781 TTTTTCAA---TATCACTTTACCTTTATAATTGAGGTCTC-TAA
1 TTTTTCAATCCTAT-TTTTTACCTTTATAATTGAGG-CCCAAAA
* * *
27821 TTTTTCAATCATAGTTTTTACTTTTATA
1 TTTTTCAATCCTATTTTTTACCTTTATA
27849 GTTTAAGCCC
Statistics
Matches: 118, Mismatches: 27, Indels: 25
0.69 0.16 0.15
Matches are distributed among these distances:
40 9 0.08
41 17 0.14
42 15 0.13
43 32 0.27
44 12 0.10
45 14 0.12
46 17 0.14
47 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (42 bp):
TTTTTCAATCCTATTTTTTACCTTTATAATTGAGGCCCAAAA
Found at i:29679 original size:22 final size:22
Alignment explanation
Indices: 29654--29704 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
29644 AACATTGTCG
29654 GGAAGCAATCACAAGGTTTCCC
1 GGAAGCAATCACAAGGTTTCCC
29676 GGAAGCAATCACAAGGTTTCCC
1 GGAAGCAATCACAAGGTTTCCC
*
29698 GTAAGCA
1 GGAAGCA
29705 TATTGTCGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (22 bp):
GGAAGCAATCACAAGGTTTCCC
Found at i:37322 original size:23 final size:23
Alignment explanation
Indices: 37286--37349 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
37276 CAGCTCATAT
37286 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
37309 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
37332 AAATACACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
37350 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:39156 original size:19 final size:20
Alignment explanation
Indices: 39132--39179 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
39122 AATGATTTTC
*
39132 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
39151 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
39171 TTTTGAAAA
1 TTTTGAAAA
39180 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:42331 original size:19 final size:19
Alignment explanation
Indices: 42291--42333 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42281 TAATGTAAAA
*
42291 ACATATAATAACATATAAC
1 ACATATAATAACATACAAC
*
42310 ACATATAATAATA-ACAACC
1 ACATATAATAACATACAA-C
42329 ACATA
1 ACATA
42334 ATCTTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (19 bp):
ACATATAATAACATACAAC
Found at i:42703 original size:18 final size:18
Alignment explanation
Indices: 42680--42722 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
42670 GAAATATTGA
42680 TGCATCGGCACCCCTTAC
1 TGCATCGGCACCCCTTAC
42698 TGCATCGGCACCCCTTAC
1 TGCATCGGCACCCCTTAC
42716 TGCATCG
1 TGCATCG
42723 ATGCACCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.42, G:0.19, T:0.23
Consensus pattern (18 bp):
TGCATCGGCACCCCTTAC
Found at i:48451 original size:26 final size:24
Alignment explanation
Indices: 48422--48483 Score: 56
Period size: 26 Copynumber: 2.5 Consensus size: 24
48412 TTGGTGGCCA
48422 AATTTGACCAATTTTGCCACCCCATT
1 AATTTGACCAATTTTGCCA-CCCA-T
** *
48448 AATTCCACCAA-ATTGCCACCCAT
1 AATTTGACCAATTTTGCCACCCAT
48471 AATGTTGA-CAATT
1 AAT-TTGACCAATT
48484 GATGCAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
23 7 0.25
24 6 0.21
25 6 0.21
26 9 0.32
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.31
Consensus pattern (24 bp):
AATTTGACCAATTTTGCCACCCAT
Found at i:54463 original size:30 final size:28
Alignment explanation
Indices: 54429--54485 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
54419 CAATTTTTTG
* *
54429 GCCCATTAGGGTATTCGGGTTTTTTATTTA
1 GCCCATTAGGATA-TCCGG-TTTTTATTTA
54459 GCCCATTAGGATATCCGGTTTTTATTT
1 GCCCATTAGGATATCCGGTTTTTATTT
54486 TGGGTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.36
29 4 0.16
30 12 0.48
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.46
Consensus pattern (28 bp):
GCCCATTAGGATATCCGGTTTTTATTTA
Found at i:59693 original size:2 final size:2
Alignment explanation
Indices: 59684--59729 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
59674 TAAAAAAACT
59684 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59725 TA TA T
1 TA TA T
59730 TAAAAAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.