Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004838.1 Hibiscus syriacus cultivar Beakdansim tig00010906_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: 54575
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1988 original size:23 final size:24
Alignment explanation
Indices: 1960--2007 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
1950 AAAAGCTGCA
1960 TCATCATAAATACC-AACATAGTC
1 TCATCATAAATACCAAACATAGTC
1983 TCATCATAAATACCAAACATAGTC
1 TCATCATAAATACCAAACATAGTC
2007 T
1 T
2008 GTCGTCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (24 bp):
TCATCATAAATACCAAACATAGTC
Found at i:2226 original size:24 final size:24
Alignment explanation
Indices: 2178--2222 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
2168 TTCGATTAGT
2178 TTTTTTAAATTTTAATATATATTA
1 TTTTTTAAATTTTAATATATATTA
*
2202 TTTTTT--ATTTTTATATATATT
1 TTTTTTAAATTTTAATATATATT
2223 TTATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTTAAATTTTAATATATATTA
Found at i:2231 original size:22 final size:22
Alignment explanation
Indices: 2186--2231 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2176 GTTTTTTTAA
*
2186 ATTTTAATATATATTATTTTTT
1 ATTTTAATATATATTATTTATT
*
2208 ATTTTTATATATATT-TTATATT
1 ATTTTAATATATATTATT-TATT
2230 AT
1 AT
2232 ATGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTAATATATATTATTTATT
Found at i:8428 original size:41 final size:38
Alignment explanation
Indices: 8382--8457 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 38
8372 GAATGAAAAA
8382 TTTGTTAACTACATAATTAAAATTTATAATAATTTTATAAT
1 TTTGTTAACTACAT-ATT--AATTTATAATAATTTTATAAT
**
8423 TTTGTTAACTACATATTTTTTTATAATAATTTTAT
1 TTTGTTAACTACATATTAATTTATAATAATTTTAT
8458 GATTGAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 16 0.48
40 3 0.09
41 14 0.42
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (38 bp):
TTTGTTAACTACATATTAATTTATAATAATTTTATAAT
Found at i:10405 original size:43 final size:43
Alignment explanation
Indices: 10281--10405 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 43
10271 TTAAACTAGA
* * * *
10281 GGCCTAAATTATAAAAGTAAAAAGTGGGAATG-AAAAATTAGG
1 GGCCTCAATTATAAAAGTAAGAAGTGAGATTGAAAAAATTAGG
* *
10323 GGCTTCAATTAT-AAGGT-AGAAAGTGAGATT-AAAATAATTAGG
1 GGCCTCAATTATAAAAGTAAG-AAGTGAGATTGAAAA-AATTAGG
* *
10365 GGCCTCAATTATAAATGTAAGAAGTGATATTGAAAAAATTA
1 GGCCTCAATTATAAAAGTAAGAAGTGAGATTGAAAAAATTA
10406 AAGGTCTCGA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
40 1 0.01
41 15 0.22
42 28 0.41
43 18 0.26
44 6 0.09
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (43 bp):
GGCCTCAATTATAAAAGTAAGAAGTGAGATTGAAAAAATTAGG
Found at i:11536 original size:28 final size:28
Alignment explanation
Indices: 11496--11578 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
11486 CTCTAACACT
* *
11496 AGAATATCTATGTAATTTCAATTCATAC
1 AGAATATATATGTAACTTCAATTCATAC
* *
11524 AGAATATATATGTAACTTCAGTTTC-TAT
1 AGAATATATATGTAACTTCA-ATTCATAC
* *
11552 AGAAAATATAGGTAACTTCAATTCATA
1 AGAATATATATGTAACTTCAATTCATA
11579 TTTTTAACAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 3 0.07
28 40 0.87
29 3 0.07
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (28 bp):
AGAATATATATGTAACTTCAATTCATAC
Found at i:16481 original size:12 final size:13
Alignment explanation
Indices: 16451--16483 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
16441 ATAAAAATAT
16451 AAATAATATTTATA
1 AAAT-ATATTTATA
16465 AAATATATTTA-A
1 AAATATATTTATA
16477 AAATATA
1 AAATATA
16484 CTTTTTACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 7 0.37
14 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATATATTTATA
Found at i:17542 original size:31 final size:32
Alignment explanation
Indices: 17507--17583 Score: 111
Period size: 31 Copynumber: 2.4 Consensus size: 32
17497 ATTAACATCG
17507 AGTGACCAATTTATTACAAATCGAT-AATGTT
1 AGTGACCAATTTATTACAAATCGATAAATGTT
* *
17538 AGTGACCAATTTGTTACAAATTGATAAATGTT
1 AGTGACCAATTTATTACAAATCGATAAATGTT
* *
17570 AATGACCTATTTAT
1 AGTGACCAATTTAT
17584 AACTTTTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 23 0.57
32 17 0.43
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (32 bp):
AGTGACCAATTTATTACAAATCGATAAATGTT
Found at i:29314 original size:15 final size:16
Alignment explanation
Indices: 29294--29325 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29284 ATGTTTGGTG
29294 TAATTTATTT-TAAAA
1 TAATTTATTTATAAAA
29309 TAATTTATTTATAAAA
1 TAATTTATTTATAAAA
29325 T
1 T
29326 TTAATGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTATTTATAAAA
Found at i:29749 original size:138 final size:138
Alignment explanation
Indices: 29587--29857 Score: 533
Period size: 138 Copynumber: 2.0 Consensus size: 138
29577 TTTGAAGTAA
29587 TTAATATAAACTATTTGTAAAATTTAATTGAGTTAATTGCATCACATGTCCTTAAATTAGTCCCT
1 TTAATATAAACTATTTGTAAAATTTAATTGAGTTAATTGCATCACATGTCCTTAAATTAGTCCCT
29652 AAATTTTAACACATTTCAATTTCATCACTAAACTATGACTATCATTCTACATTAGTCCTCAAATT
66 AAATTTTAACACATTTCAATTTCATCACTAAACTATGACTATCATTCTACATTAGTCCTCAAATT
29717 TGTAAACT
131 TGTAAACT
29725 TTAATATAAACTATTTGTAAAATTTAATTGAGTTAATTGCATCACATGTCCTTAAATTAGTCCCT
1 TTAATATAAACTATTTGTAAAATTTAATTGAGTTAATTGCATCACATGTCCTTAAATTAGTCCCT
*
29790 AAATTTTAACACATTTCAATTTTATCACTAAACTATGACTATCATTCTACATTAGTCCTCAAATT
66 AAATTTTAACACATTTCAATTTCATCACTAAACTATGACTATCATTCTACATTAGTCCTCAAATT
29855 TGT
131 TGT
29858 TAACATTTCA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (138 bp):
TTAATATAAACTATTTGTAAAATTTAATTGAGTTAATTGCATCACATGTCCTTAAATTAGTCCCT
AAATTTTAACACATTTCAATTTCATCACTAAACTATGACTATCATTCTACATTAGTCCTCAAATT
TGTAAACT
Found at i:30712 original size:66 final size:66
Alignment explanation
Indices: 30606--30735 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
30596 TAGGTCCATA
* * *
30606 AGGAATTACCAGTCGGTGCTAAACGTATACAAGGAATTACCAGCAACAACTGAACCTACCAGAGA
1 AGGAATTACCAGTCAGTGCTAAACCTATACAAGGAATTACCAGCAACAACTAAACCTACCAGAGA
30671 T
66 T
* * * * *
30672 AGGAATTACCAGTCAGTGTTGAACCTATACAAGGAATTACCAGCATCGACTAAACCTGCCAGAG
1 AGGAATTACCAGTCAGTGCTAAACCTATACAAGGAATTACCAGCAACAACTAAACCTACCAGAG
30736 TCTTCACACC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (66 bp):
AGGAATTACCAGTCAGTGCTAAACCTATACAAGGAATTACCAGCAACAACTAAACCTACCAGAGA
T
Found at i:31795 original size:27 final size:28
Alignment explanation
Indices: 31741--31796 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
31731 GCTTGGAGAT
*
31741 ATTTTAGGTCATTTTACACTTTAAGGGC
1 ATTTTAGGTCATTTTACACTTCAAGGGC
*
31769 ATTTT-GGTCATTTTACACTTCAGGGGC
1 ATTTTAGGTCATTTTACACTTCAAGGGC
31796 A
1 A
31797 ATTATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (28 bp):
ATTTTAGGTCATTTTACACTTCAAGGGC
Found at i:38049 original size:32 final size:31
Alignment explanation
Indices: 38013--38089 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
38003 CGGGGCCGTG
*
38013 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
38045 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
38076 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
38090 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:38072 original size:63 final size:63
Alignment explanation
Indices: 37966--38089 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
37956 CACTAAGGGA
* * ** *
37966 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
38029 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
38090 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:38971 original size:7 final size:7
Alignment explanation
Indices: 38959--38996 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
38949 GTCAAAGAAA
38959 GTCAACG
1 GTCAACG
38966 GTCAACG
1 GTCAACG
38973 GTCAACG
1 GTCAACG
38980 GTCAACG
1 GTCAACG
38987 GTCAACG
1 GTCAACG
38994 GTC
1 GTC
38997 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:39014 original size:22 final size:22
Alignment explanation
Indices: 38986--39050 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
38976 AACGGTCAAC
38986 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
39008 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
39030 GGTCAACAGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
39051 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:39050 original size:5 final size:5
Alignment explanation
Indices: 38993--39033 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
38983 AACGGTCAAC
*
38993 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
39034 AACAGTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:39073 original size:19 final size:18
Alignment explanation
Indices: 39047--39136 Score: 110
Period size: 19 Copynumber: 4.8 Consensus size: 18
39037 AGTCGGGTCG
39047 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
39065 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
39084 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
39103 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
39123 GGTCAAACCGGTCA
1 GGTCAGACCGGTCA
39137 GAATCGGTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.10
19 48 0.76
20 9 0.14
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:39144 original size:29 final size:29
Alignment explanation
Indices: 39091--39164 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
39081 ACCGAGTCAG
39091 ACCGGTCAAACCGGTTCGAACCGGTTG-AA
1 ACCGGTCAAACCGG-TCGAACCGGTTGAAA
*
39120 ACCGGTCAAACCGGTCAGAATCGGTTGAAA
1 ACCGGTCAAACCGGTC-GAACCGGTTGAAA
*
39150 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
39165 TTCCAGCAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 16 0.39
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.18
Consensus pattern (29 bp):
ACCGGTCAAACCGGTCGAACCGGTTGAAA
Found at i:39165 original size:9 final size:9
Alignment explanation
Indices: 39047--39164 Score: 101
Period size: 9 Copynumber: 12.3 Consensus size: 9
39037 AGTCGGGTCG
*
39047 GGTCAGACC
1 GGTCAAACC
39056 GGTCAAACC
1 GGTCAAACC
*
39065 GGCTCAGACC
1 GG-TCAAACC
39075 GGTCAAACC
1 GGTCAAACC
*
39084 GAGTCAGACC
1 G-GTCAAACC
39094 GGTCAAACC
1 GGTCAAACC
*
39103 GGTTCGAACC
1 GG-TCAAACC
*
39113 GGTTGAAACC
1 GG-TCAAACC
39123 GGTCAAACC
1 GGTCAAACC
*
39132 GGTCAGAATC
1 GGTCA-AACC
*
39142 GGTTGAAAACC
1 GG-T-CAAACC
*
39153 GGTTAAACC
1 GGTCAAACC
39162 GGT
1 GGT
39165 TTCCAGCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
9 45 0.50
10 38 0.42
11 6 0.07
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:45444 original size:32 final size:31
Alignment explanation
Indices: 45408--45484 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
45398 TCGGGCCGTG
*
45408 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
45440 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
45471 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
45485 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:46365 original size:7 final size:7
Alignment explanation
Indices: 46353--46383 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
46343 GTCAAAGAAA
46353 GTCAACG
1 GTCAACG
46360 GTCAACG
1 GTCAACG
46367 GTCAACG
1 GTCAACG
46374 GTCAACG
1 GTCAACG
46381 GTC
1 GTC
46384 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:46401 original size:22 final size:22
Alignment explanation
Indices: 46373--46437 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
46363 AACGGTCAAC
46373 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
46395 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
46417 GGTCAACAGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
46438 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:46437 original size:5 final size:5
Alignment explanation
Indices: 46380--46420 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
46370 AACGGTCAAC
*
46380 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
46421 AACAGTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:46460 original size:19 final size:18
Alignment explanation
Indices: 46434--46523 Score: 110
Period size: 19 Copynumber: 4.8 Consensus size: 18
46424 AGTCGGGTCG
46434 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
46452 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
46471 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
46490 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
46510 GGTCAAACCGGTCA
1 GGTCAGACCGGTCA
46524 GAATCGGTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.10
19 48 0.76
20 9 0.14
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:46531 original size:29 final size:29
Alignment explanation
Indices: 46478--46551 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
46468 ACCGAGTCAG
46478 ACCGGTCAAACCGGTTCGAACCGGTTG-AA
1 ACCGGTCAAACCGG-TCGAACCGGTTGAAA
*
46507 ACCGGTCAAACCGGTCAGAATCGGTTGAAA
1 ACCGGTCAAACCGGTC-GAACCGGTTGAAA
*
46537 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
46552 TTCCAGCAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 16 0.39
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.18
Consensus pattern (29 bp):
ACCGGTCAAACCGGTCGAACCGGTTGAAA
Found at i:46552 original size:9 final size:9
Alignment explanation
Indices: 46434--46551 Score: 101
Period size: 9 Copynumber: 12.3 Consensus size: 9
46424 AGTCGGGTCG
*
46434 GGTCAGACC
1 GGTCAAACC
46443 GGTCAAACC
1 GGTCAAACC
*
46452 GGCTCAGACC
1 GG-TCAAACC
46462 GGTCAAACC
1 GGTCAAACC
*
46471 GAGTCAGACC
1 G-GTCAAACC
46481 GGTCAAACC
1 GGTCAAACC
*
46490 GGTTCGAACC
1 GG-TCAAACC
*
46500 GGTTGAAACC
1 GG-TCAAACC
46510 GGTCAAACC
1 GGTCAAACC
*
46519 GGTCAGAATC
1 GGTCA-AACC
*
46529 GGTTGAAAACC
1 GG-T-CAAACC
*
46540 GGTTAAACC
1 GGTCAAACC
46549 GGT
1 GGT
46552 TTCCAGCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
9 45 0.50
10 38 0.42
11 6 0.07
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:51252 original size:16 final size:16
Alignment explanation
Indices: 51231--51262 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51221 TTAAAATGTC
51231 ATGAATGTATGCGTCT
1 ATGAATGTATGCGTCT
51247 ATGAATGTATGCGTCT
1 ATGAATGTATGCGTCT
51263 GTAGTGCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (16 bp):
ATGAATGTATGCGTCT
Done.